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Pete S, Roy N, Kar B, Paira P. Construction of homo and heteronuclear Ru(II), Ir(III) and Re(I) complexes for target specific cancer therapy. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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2
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Das U, Kar B, Pete S, Paira P. Ru(ii), Ir(iii), Re(i) and Rh(iii) based complexes as next generation anticancer metallopharmaceuticals. Dalton Trans 2021; 50:11259-11290. [PMID: 34342316 DOI: 10.1039/d1dt01326b] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Several anticancer drugs such as cisplatin, and its analogues, epirubicin, and doxorubicin are well known for their anticancer activity but the therapeutic value of these drugs comes with certain side effects and they cannot distinguish between normal and cancer cells. Thus, a major challenge for researchers around the world is to develop an anticancer drug with the least toxicity and more target specificity. With the successful reporting of NAMI-A and KP1019, a new path has emerged in the anticancer field. Recently, several Ru(ii) complexes have been reported for their anticancer activity due to their enhanced cellular uptake and selectivity towards cancer cells. Apart from the Ru(ii) complexes, a large amount of research has been carried out with Ir(iii), Re(i), and Rh(iii) based complexes, which exhibited promising anticancer activity. The present review reports various Ru(ii), Ir(iii), Re(i), and Rh(iii) based complexes for their anticancer activity based on their cytotoxicity profiles, biological targets and mechanism of action.
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Affiliation(s)
- Utpal Das
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore-632014, Tamilnadu, India.
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3
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Seedorf T, Kirschning A, Solga D. Natural and Synthetic Oligoarylamides: Privileged Structures for Medical Applications. Chemistry 2021; 27:7321-7339. [PMID: 33481284 PMCID: PMC8251530 DOI: 10.1002/chem.202005086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
The term "privileged structure" refers to a single molecular substructure or scaffold that can serve as a starting point for high-affinity ligands for more than one receptor type. In this report, a hitherto overlooked group of privileged substructures is addressed, namely aromatic oligoamides, for which there are natural models in the form of cystobactamids, albicidin, distamycin A, netropsin, and others. The aromatic and heteroaromatic core, together with a flexible selection of substituents, form conformationally well-defined scaffolds capable of specifically binding to conformationally well-defined regions of biomacromolecules such as helices in proteins or DNA often by acting as helices mimics themselves. As such, these aromatic oligoamides have already been employed to inhibit protein-protein and nucleic acid-protein interactions. This article is the first to bring together the scattered knowledge about aromatic oligoamides in connection with biomedical applications.
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Affiliation(s)
- Tim Seedorf
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Danny Solga
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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4
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Sudhindra P, Ajay Sharma S, Roy N, Moharana P, Paira P. Recent advances in cytotoxicity, cellular uptake and mechanism of action of ruthenium metallodrugs: A review. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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Prabhu Kumar K, Vasantha Kumar B, Kumar PR, Butcher RJ, Vivek H, Suchetan P, Revanasiddappa H, Foro S. Synthesis, characterization, CT‐DNA binding and docking studies of novel selenated ligands and their palladium complexes. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- K.M. Prabhu Kumar
- Department of Studies and Research in ChemistryTumkur University Tumkur Karnataka 572 103 India
| | - B.C. Vasantha Kumar
- Department of Studies in ChemistryUniversity of Mysore Mysuru Karnataka 570 006 India
| | - P. Raghavendra Kumar
- Department of Studies and Research in ChemistryTumkur University Tumkur Karnataka 572 103 India
| | | | - H.K. Vivek
- Faculty of Natural SciencesAdichunchanagiri University B. G. Ngara Mandya Karnataka India
| | - P.A. Suchetan
- Department of Studies and Research in ChemistryTumkur University Tumkur Karnataka 572 103 India
| | - H.D. Revanasiddappa
- Department of Studies in ChemistryUniversity of Mysore Mysuru Karnataka 570 006 India
| | - Sabine Foro
- Institute of Materials ScienceDarmstadt University of Technology Petersenstr. 23 D‐64287 Darmstadt Germany
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6
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Abouzeid LA, El-Subbagh HI. DNA binding of ethyl 2-substituted aminothiazole-4-carboxylate analogues: A molecular modeling approach to predict their antitumor activity. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2015. [DOI: 10.1016/j.fjps.2015.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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7
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Hegde M, Sharath Kumar KS, Thomas E, Ananda H, Raghavan SC, Rangappa KS. A novel benzimidazole derivative binds to the DNA minor groove and induces apoptosis in leukemic cells. RSC Adv 2015. [DOI: 10.1039/c5ra16605e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In the present study, we have synthesized various benzimidazole derivatives, evaluated their potential to act as DNA minor groove binder and tested their chemotherapeutic efficacy.
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Affiliation(s)
- Mahesh Hegde
- Department of Studies in Chemistry
- Manasagangotri, University of Mysore
- Mysuru-570006, India
| | | | - Elizabeth Thomas
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Hanumappa Ananda
- Department of Studies in Chemistry
- Manasagangotri, University of Mysore
- Mysuru-570006, India
| | - Sathees C. Raghavan
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012, India
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8
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Singh M, Sur S, Rastogi GK, Jayaram B, Tandon V. Bi and tri-substituted phenyl rings containing bisbenzimidazoles bind differentially with DNA duplexes: a biophysical and molecular simulation study. MOLECULAR BIOSYSTEMS 2014; 9:2541-53. [PMID: 23921527 DOI: 10.1039/c3mb70169g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recently synthesis of programmable DNA ligands which can regulate transcription factors have increased the interest of researchers on the functional ability of DNA interacting compounds. A series of DNA interacting compounds are being designed which can differentiate between GC and AT rich DNA. In this study, we have studied the specificity of a few novel bisbenzimidazoles having different bi/tri-substituted phenyl rings, with DNA duplexes using spectroscopic methods. This study entails an integrative approach where we combine biophysical methods and molecular dynamics simulation studies to establish suitable scaffolds to target A/T DNA. We have designed a few analogues of Hoechst 33342 viz.; dimethoxy (DMA), trimethoxy (TMA), dichloro (DCA) and difluoro (DFA) functionalities and performed molecular docking of newly designed analogues with biologically relevant AT and GC rich DNA sequences. The docking studies, along with molecular dynamics (MD) simulations of d(ATATATATATATATAT)2, d(GA4T4C)2, d(GT4A4C)2 and GC rich sequence: d(GCGCGCGCGCGCGCGC)2 complexed with DMA, TMA and DFA, showed that these molecules have higher binding affinity towards AT rich DNA. None of these compounds exhibited an affinity to GC rich DNA rather we observed that these compounds destabilize GC rich DNA. The binding was characterized by strong stabilization of the polynucleotides against thermal strand separation in thermal melting experiments. New insights into the molecules binding to DNA have emerged from these studies. All the DNA binding ligands stabilized d(GA4T4C)2 and d(GT4A4C)2 more out of the five oligomers used for the study, suggesting that these ligands bind 'A4T4' and 'T4A4' strongly as compared to 'ATAT' base pairs.
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Affiliation(s)
- Manish Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi, India
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9
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DNA-binding of nickel(II), copper(II) and zinc(II) complexes: Structure–affinity relationships. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.023] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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10
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Chitrapriya N, Kim R, Jang YJ, Cho DW, Han SW, Kim SK. Sequence Dependent Binding Modes of the ΔΔ- and ΛΛ-binuclear Ru(II) Complexes to poly[d(G-C) 2] and poly[d(A-T) 2]. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Novel amidines and analogues as promising agents against intracellular parasites: a systematic review. Parasitology 2013; 140:929-51. [PMID: 23561006 DOI: 10.1017/s0031182013000292] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Parasitic protozoa comprise diverse aetiological agents responsible for important diseases in humans and animals including sleeping sickness, Chagas disease, leishmaniasis, malaria, toxoplasmosis and others. They are major causes of mortality and morbidity in tropical and subtropical countries, and are also responsible for important economic losses. However, up to now, for most of these parasitic diseases, effective vaccines are lacking and the approved chemotherapeutic compounds present high toxicity, increasing resistance, limited efficacy and require long periods of treatment. Many of these parasitic illnesses predominantly affect low-income populations of developing countries for which new pharmaceutical alternatives are urgently needed. Thus, very low research funding is available. Amidine-containing compounds such as pentamidine are DNA minor groove binders with a broad spectrum of activities against human and veterinary pathogens. Due to their promising microbicidal activity but their rather poor bioavailability and high toxicity, many analogues and derivatives, including pro-drugs, have been synthesized and screened in vitro and in vivo in order to improve their selectivity and pharmacological properties. This review summarizes the knowledge on amidines and analogues with respect to their synthesis, pharmacological profile, mechanistic and biological effects upon a range of intracellular protozoan parasites. The bulk of these data may contribute to the future design and structure optimization of new aromatic dicationic compounds as novel antiparasitic drug candidates.
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12
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Khan GS, Shah A, Zia-ur-Rehman, Barker D. Chemistry of DNA minor groove binding agents. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 115:105-18. [DOI: 10.1016/j.jphotobiol.2012.07.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/04/2012] [Accepted: 07/07/2012] [Indexed: 12/19/2022]
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13
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Lin CY, Yang YT, Ong CW. Synthesis of Chiral Pyrrolidine Isostere Inserted into Pyrrole Polyamide Skeleton. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201100603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Ong CW, Yang YT, Liu MC, Fox KR, Liu PH, Tung HW. Synthesis of directly linked diazine isosteres of pyrrole-polyamide that photochemically cleave DNA. Org Biomol Chem 2012; 10:1040-6. [DOI: 10.1039/c1ob06803b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Zabost E, Nowicka AM, Mazerska Z, Stojek Z. Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand–dsDNA complexes of various types of binding. An electrochemical study. Phys Chem Chem Phys 2012; 14:3408-13. [DOI: 10.1039/c2cp23824a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Lo ATS, Salam NK, Hibbs DE, Rutledge PJ, Todd MH. Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal. PLoS One 2011; 6:e17446. [PMID: 21573061 PMCID: PMC3090394 DOI: 10.1371/journal.pone.0017446] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/03/2011] [Indexed: 01/17/2023] Open
Abstract
Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed "click" reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail.
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Affiliation(s)
- Anthony T. S. Lo
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Noeris K. Salam
- Schrödinger, Inc., New York, New York, United States of
America
| | - David E. Hibbs
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales,
Australia
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Matthew H. Todd
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
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17
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Rao L, West TK, Saluta G, Kucera GL, Bierbach U. Probing platinum-adenine-n3 adduct formation with DNA minor-groove binding agents. Chem Res Toxicol 2010; 23:1148-50. [PMID: 20578739 DOI: 10.1021/tx100170p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Me-lex(py/py), an adenine-N3-selective alkylating agent, and the reversible minor-groove binder netropsin were used to probe the formation of unusual minor-groove adducts by the cytotoxic hybrid agent PT-ACRAMTU ([PtCl(en)(ACRAMTU)](NO(3))(2); en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea). PT-ACRAMTU was found by chemical footprinting to inhibit specific Me-lex-mediated DNA cleavage at several adenine sites but not at nonspecific guanine, which is consistent with the platination of adenine-N3. In a cell proliferation assay, a significant decrease in cytotoxicity was observed for PT-ACRAMTU, when cancer cells were pretreated with netropsin, suggesting that minor-groove adducts in cellular DNA contribute to the biological activity of the hybrid agent.
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Affiliation(s)
- Lu Rao
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
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18
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Pandya P, Islam MM, Kumar GS, Jayaram B, Kumar S. DNA minor groove binding of small molecules: Experimental and computational evidence. J CHEM SCI 2010. [DOI: 10.1007/s12039-010-0029-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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20
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Wolter FE, Schneider K, Davies BP, Socher ER, Nicholson G, Seitz O, Süssmuth RD. Total Synthesis of Proximicin A−C and Synthesis of New Furan-Based DNA Binding Agents. Org Lett 2009; 11:2804-7. [DOI: 10.1021/ol901003p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Falko E. Wolter
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Kathrin Schneider
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Brian P. Davies
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Elke R. Socher
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Graeme Nicholson
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Oliver Seitz
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Roderich D. Süssmuth
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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21
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Schneider K, Keller S, Wolter F, Röglin L, Beil W, Seitz O, Nicholson G, Bruntner C, Riedlinger J, Fiedler HP, Süssmuth R. Proximicin A, B und C – antitumoraktive Furananaloga des Netropsins aus dem marinen ActinomycetenVerrucosispora induzieren die Hochregulation von p53 und des Cyclinkinase-Inhibitors p21. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Schneider K, Keller S, Wolter F, Röglin L, Beil W, Seitz O, Nicholson G, Bruntner C, Riedlinger J, Fiedler HP, Süssmuth R. Proximicins A, B, and C—Antitumor Furan Analogues of Netropsin from the Marine ActinomyceteVerrucosispora Induce Upregulation of p53 and the Cyclin Kinase Inhibitor p21. Angew Chem Int Ed Engl 2008; 47:3258-61. [DOI: 10.1002/anie.200705295] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Hooda J, Bednarski D, Irish L, Firestine SM. Synthesis and testing of a triaza-cyclopenta[b]phenanthrene scaffold as a DNA binding agent. Bioorg Med Chem 2006; 14:1902-9. [PMID: 16298133 DOI: 10.1016/j.bmc.2005.10.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Revised: 10/24/2005] [Accepted: 10/25/2005] [Indexed: 11/17/2022]
Abstract
A novel DNA binding agent based upon a triaza-cyclopenta[b]phenanthrene scaffold, compound 1, has been synthesized. dsDNA binding analysis of this compound using the ethidium bromide displacement assay indicated a preference for GC-rich sequences. However, equilibrium dialysis experiments against a variety of nucleic acids showed that the target compound bound about 20-fold tighter to G-quartet DNA than to dsDNA under physiological salt concentrations. The binding of 1 to G-quartet DNA was verified by the ability of the compound to promote the formation of the quartet and to compete with TmPyP4 for binding to the quadruplex. Given the importance of G-quartet binding agents in the treatment of cancer and in the understanding of drug-DNA interactions, 1 and its related analogs should find utility as a new class of G-quartet specific agents.
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Affiliation(s)
- Jaipal Hooda
- Wayne State University, Eugene Applebaum College of Pharmacy and Health Science, Department of Pharmaceutical Sciences, 259 Mack Avenue, Detroit, MI 48201, USA
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24
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Interaction of HIV-1 Reverse Transcriptase with New Minor Groove Binders and Their Conjugates with Oligonucleotides. Mol Biol 2005. [DOI: 10.1007/s11008-005-0057-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Affiliation(s)
| | - Burkhard König
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany
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Chaltin P, Borgions F, Rozenski J, Van Aerschot A, Herdewijn P. New dsDNA-Binding Hybrid Molecules Combining an Unnatural Peptide and an Intercalating Moiety. Helv Chim Acta 2003. [DOI: 10.1002/hlca.200390054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Marchini S, Broggini M, Sessa C, D'Incalci M. Development of distamycin-related DNA binding anticancer drugs. Expert Opin Investig Drugs 2001; 10:1703-14. [PMID: 11772279 DOI: 10.1517/13543784.10.9.1703] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The relatively low therapeutic index of the clinically used alkylating agents is probably related to the fact that these compounds cause DNA damage in a relatively unspecific manner, mainly involving guanine-cytosine rich stretches of DNA present in virtually all genes, therefore inducing unselective growth inhibition and death, both in neoplastic and in highly proliferative normal tissues. These considerations explain why in the last twenty years there has been an increasing interest in the identification of compounds which can target DNA with a much higher degree of sequence specificity than that of conventional alkylators. Minor groove binders (MGBs) are one of the most widely studied class of alkylating agents characterised by a high level of sequence specificity. The prototype of this class of drugs is distamycin A which is an antiviral compound able to interact, non-covalently, in theminor groove of DNA in A-T rich regions. It is not cytotoxic against tumour cells and thus has been used as a carrier for targeting cytotoxic alkylating moieties in theminor groove of DNA. The benzoyl mustard derivative of distamycin A, tallimustine, was found to be able to alkylate the N(3) of adenine in theminor groove of DNA only in the target hexamer 5'-TTTTGA or 5'-TTTTAA. Tallimustine was investigated in the clinic and was not successful because it causes severe bone marrow toxicity. The screening of other distamycin derivatives, which maintain antitumour activity and exhibit much lower toxicity against human bone marrow cells than tallimustine led to the identification of brostallicin (PNU-166196) which is currently under early clinical investigation. Although MGBs which bind DNA in A-T rich regions have not fulfilled the expectations, it is too early to draw definitive conclusions on this class of compounds. The peculiar bone-marrow toxicity observed in the clinic both with tallimustine or with CC-1065 derivatives is not necessarily a feature of all MGBs, as indicated by recent evidence obtained with brostallicin and other structurally unrelated MGBs (e.g., ET-743).
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Affiliation(s)
- S Marchini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Via Eritrea, 62- 20157 Milan, Italy
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28
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Bugreev DV, Vasyutina EL, Ryabinin VA, Sinyakov AN, Buneva VN, Nevinsky GA. Inhibition of human DNA topoisomerase I by new DNA minor groove ligands: derivatives of oligo-1,3-thiazolecarboxamides. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:137-47. [PMID: 11446589 DOI: 10.1089/108729001300338663] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A series of novel thiazole-containing oligopeptides (oligo-1,3-thiazolecarboxamides) interesting specifically with the minor groove of DNA was shown to inhibit human DNA topoisomerase I (topo I). Inhibitory effects of thiazole-containing oligopeptides (TCO) increase with the number of thiazole units in such compounds. Inhibitory properties of TCO containing 3 or 4 thiazole units were shown to be 3-10 times better than those of the well-known natural antibiotic, distamycin A containing pyrrole rings. The structure of various additional groups attached to the N-terminus and C-terminus of TCO had no significant effect on TCO interaction with the complex of DNA and topo I. TCO were shown to be capable of binding with double-stranded DNA (dsDNA), and the majority of TCO analyzed were more effective in binding with dsDNA than distamycin A. Possible reasons for the different effects of distamycin A and TCO on the reaction of relaxation catalyzed by topo I are discussed.
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Affiliation(s)
- D V Bugreev
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of the Russian Academy of Sciences
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Wemmer DE. Designed sequence-specific minor groove ligands. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 29:439-61. [PMID: 10940255 DOI: 10.1146/annurev.biophys.29.1.439] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the past decade, a general design for sequence-specific minor groove ligands has evolved, based on the natural products distamycin and netropsin. By utilizing a basic set of design rules for connecting pyrrole, imidazole, and hydroxypyrrole modules, new ligands can be prepared to target almost any sequence of interest with both high affinity and specificity. In this review we present the design rules with a brief history of how they evolved. The structural basis for sequence-specific recognition is explained, together with developments that allow linking of recognition modules that enable targeting of long DNA sequences. Examples of the affinity and specificity that can be achieved with a number of variations on the basic design are given. Recently these molecules have been used to compete with proteins both in vitro and in vivo, and a brief description of the experimental results are given.
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Affiliation(s)
- D E Wemmer
- Department of Chemistry, University of California, Berkeley, USA.
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30
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Sapse AM, Rothchild R, Lown JW. Semi-empirical, ab initio and molecular modeling studies on the DNA binding of a calicheamicinone-polyamide conjugate. J Biomol Struct Dyn 2000; 18:423-31. [PMID: 11149518 DOI: 10.1080/07391102.2000.10506678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
AM1 semi-empirical and ab initio calculations were performed on certain synthetic polyamide conjugates of the aglycone of the minor groove binding antibiotic calicheamicin. Geometry optimized conformations and heats of formation were obtained. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)n and to (G)n x (C)n sequences were studied and the energies of binding were compared to each other. The results can be utilized in the design of novel enediyne-based drugs.
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Affiliation(s)
- A M Sapse
- City University of New York, Graduate School and John Jay College, NY 10022, USA
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31
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Ryabinin VA, Zakharova OD, Yurchenko EY, Timofeeva OA, Martyanov IV, Tokarev AA, Belanov EF, Bormotov NI, Tarrago-Litvak L, Andreola ML, Litvak S, Nevinsky GA, Sinyakov AN. Synthesis and evaluation of oligo-1,3-thiazolecarboxamide derivatives as HIV-1 reverse transcriptase inhibitors. Bioorg Med Chem 2000; 8:985-93. [PMID: 10882010 DOI: 10.1016/s0968-0896(00)00029-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A set of oligo-1,3-thiazolecarboxamide derivatives able to interact with the minor groove of nucleic acids was synthesized. These oligopeptides contained different numbers of thiazole units presenting dimethylaminopropyl or EDTA moieties on the C-terminus, and aminohexanoyl or EDTA moieties on the N-terminus. The inhibition of such compounds on HIV-1 reverse transcriptase activity was evaluated using different model template primer duplexes: DNA x DNA, RNA x DNA, DNA x RNA and RNA x RNA. The biological properties of the thiazolecarboxamide derivatives were compared to those of distamycin, another minor groove binder which contains three pyrrole rings. Similar to distamycin, the thiazole containing oligopeptides were good inhibitors of the reverse transcription reaction in the presence of DNA x DNA. But in contrast to distamycin, the oligothiazolide derivatives were able to inhibit reverse transcription in the presence of RNA x DNA or DNA x RNA template primers. Both distamycin and oligothiazolecarboxamides had low affinity for RNA x RNA duplexes. The inhibition obtained with the newly synthesized thiazolecarboxamides showed that these compounds were more powerful and versatile inhibitors of the RT-dependent polymerization than the natural minor groove binder distamycin.
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Affiliation(s)
- V A Ryabinin
- Institute of Molcular Biology, Koltsoro, Novosibirsk Region, Russia
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32
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Abstract
In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.
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Affiliation(s)
- B S Reddy
- Department of Chemistry, University of Alberta, Edmonton, Canada
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33
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Kittler L, Baguley BC, Löber G, Waring MJ. Sequence-specific interactions of minor groove binders with restriction fragments of cDNAs for H tau 40 protein and MAP kinase 2. A qualitative and quantitative footprinting study. J Mol Recognit 1999; 12:121-30. [PMID: 10398403 DOI: 10.1002/(sici)1099-1352(199903/04)12:2<121::aid-jmr450>3.0.co;2-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A series of DNA minor groove binders comprising netropsin, distamycin, the bisquaternary ammonium heterocycles SN 6999 and SN 6570, cis-diammine platinum(II)-bridged bis-netropsin, cis-diammine platinum(II)-bridged bis-distamycin and bis-glycine-linked bis-distamycin were investigated for sequence-specific interactions. The oligonucleotides used were the 154 base pair HindIII-RsaI restriction fragment of cDNA of h tau 40 protein and the 113 base pair NcoI-PvuII restriction fragment of cDNA of MAP kinase 2. Both proteins are believed to be involved in the pathology of Alzheimer's disease. For all these ligands, binding sites were localised at positions 1134-1139 (5'AATCTT3'), 1152-1156 (5'ATATT3') and 1178-1194 (5'TTTCAATCTTTTTATTT3') for the former and 720-726 (5'TATTCTT3'), 751-771 (5'AATTGTATAATAAATTTAAAA3') and 781-785 (5'TATTT3') for the latter. The AT-preference of ligand binding was obvious and footprint titration experiments were applied to estimate binding constants (Ka) for each individual binding site mentioned above. The binding strength decreases in the order netropsin > distamycin > SN 6999 approximately SN 6570>platinum-bridged netropsin or distamycin approximately bis-glycine-bridged distamycin and was found independently of the binding sites examined. GC-base pairs interspersed in short AT-tracts reduced the Ka-values by as much as two orders of magnitudes. The dependence of extended bidentate as well as of monodentate binding of netropsin and distamycin derivatives on the length of AT-stretches has been discussed.
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Affiliation(s)
- L Kittler
- Institute of Molecular Biotechnology, Beutenbergstrasse 11, D-07745 Jena, Germany.
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34
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Damayanthi Y, Praveen Reddy BS, Lown JW. Design and Synthesis of Novel Pyrrolo[2,1-c][1,4]benzodiazepine-Lexitropsin Conjugates. J Org Chem 1999; 64:290-292. [PMID: 11674116 DOI: 10.1021/jo9812072] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yalamati Damayanthi
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
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35
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Bailly C, Chaires JB. Sequence-specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues. Bioconjug Chem 1998; 9:513-38. [PMID: 9736486 DOI: 10.1021/bc980008m] [Citation(s) in RCA: 215] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- C Bailly
- INSERM U-124 et Laboratoire de Pharmacologie Antitumorale Moléculaire du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France.
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Neamati N, Mazumder A, Sunder S, Owen JM, Tandon M, Lown JW, Pommier Y. Highly potent synthetic polyamides, bisdistamycins, and lexitropsins as inhibitors of human immunodeficiency virus type 1 integrase. Mol Pharmacol 1998; 54:280-90. [PMID: 9687569 DOI: 10.1124/mol.54.2.280] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Alignment of the available human immunodeficiency virus type 1 (HIV-1) viral DNA termini [U5 and U3 long terminal repeats (LTRs)] shows a high degree of conservation and the presence of a stretch of five or six consecutive adenine and thymine (AT) sequences approximately 10 nucleotides away from each LTR end. A series of AT-selective minor-groove binders, including distamycin and bisdistamycins, bisnetropsins, novel lexitropsins, and the classic monomeric DNA binders Hoechst 33258, 4'-diamino-2-phenylindole, pentamidine, berenil, spermine, and spermidine, were tested for their inhibitory activities against HIV-1 integrase (IN). Although netropsin, distamycin, and all other monomeric DNA binders showed weak activities in the range of 50-200 microM, some of the polyamides, bisdistamycins, and lexitropsins were remarkably active at nanomolar concentrations. Bisdistamycins were 200 times less potent when the conserved AAAAT stretch present in the U5 LTR was replaced with GGGGG, consistent with the preferred binding of these drugs to AT sequences. DNase I footprinting of the U5 LTR further demonstrated the selectivity of these bisdistamycins for the conserved AT sequence. The tested compounds were more potent in Mg+2 than in Mn+2 and inhibited IN50-212 deletion mutant in disintegration assays and the formation of IN/DNA complexes. The lexitropsins also were active against HIV-2 IN. Some of the synthetic polyamides exhibited significant antiviral activity. Taken together, these data suggest that selective targeting of the U5 and U3 ends of the HIV-1 LTRs can inhibit IN function. Polyamides might represent new leads for the development of antiviral agents against acquired immune deficiency syndrome.
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Affiliation(s)
- N Neamati
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Bethesda, Maryland 20892, USA
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37
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Abstract
A new structure beings into sharp focus the structural basis for G-C base pair recognition by small ligands in the minor groove of DNA. At the same time the ability to distinguish specific sequences moves another major step forward through introduction of a new ligand modification.
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38
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Bailly C. Sequence-specific recognition and modification of double-helical DNA by minor-groove binding conjugates structurally related to netropsin and distamycin. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1067-568x(98)80007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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Bell A, Kittler L, Löber G, Zimmer C. DNA binding properties of minor groove binders and their influence on the topoisomerase II cleavage reaction. J Mol Recognit 1997; 10:245-55. [PMID: 9770648 DOI: 10.1002/(sici)1099-1352(199711/12)10:6<245::aid-jmr367>3.0.co;2-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present titrations of the human delta beta-globin gene region with DNA minor groove binders netropsin, bisnetropsin, distamycin, chromomycin and four bis-quaternary ammonium compounds in the presence of calf thymus topoisomerase II and DNase I. With increasing ligand concentration, stimulation and inhibition of enzyme activity were detected and quantitatively evaluated. Additionally we show a second type of stimulation, the appearance of strong new topoisomerase II cleavage sites at high ligand concentrations. The specific binding sites of the minor groove binders of the DNA sequence and their microscopic binding constants were determined from DNase I footprints. A binding mechanism for minor groove binders is proposed in order to explain these results especially when ligand concentration is increased.
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Affiliation(s)
- A Bell
- Institut für Molekulare Biotechnologie e. V., Jena, Germany
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40
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Burckhardt G, Simon H, Störl K, Triebel H, Walter A, Lown JW, Zimmer C. DNA binding studies and influence on the activity of DNA topoisomerases of bis-netropsins: different effects of analogs containing cis and trans ethylene linkers. J Biomol Struct Dyn 1997; 15:81-95. [PMID: 9283982 DOI: 10.1080/07391102.1997.10508948] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Binding to DNA and synthetic duplex polymers of two bifunctional netropsins and effects on supercoiled plasmid DNA as well as their inhibitory potency on DNA topoisomerases have been investigated. Characteristic differences were found in the DNA binding properties of the two bis-netropsins containing a cis and trans tether as reflected by CD, thermal melting and sedimentation measurements. CD results indicate, that the bis-netropsins interact with DNA by a two-step binding mode depending on the ligand concentration. The trans bis-netropsin may form stable complexes with different DNA's at high salt concentration, whereas for cis bis-netropsin DNA complexes the second binding step is completely abolished. The variations in the DNA binding ability of trans and cis bis-netropsin show a close relationship to the differences observed in their inhibitory effects on DNA topoisomerases. It appeared that trans bis-netropsin more strongly blocks topoisomerase activity than the cis isomer and represents the most potent inhibitor of DNA gyrase. Differences in the DNA. binding ability of the bis-netropsins and their inhibitory potency on topoisomerase activity are explained in terms of bidentate and monodentate binding mode of the trans and cis isomer, respectively.
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Affiliation(s)
- G Burckhardt
- Abteilung Molekulare Biologie, Institut für Molekularbiologie der Friedrich-Schiller-Universität, Jena, Germany
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41
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Routier S, Bernier JL, Catteau JP, Bailly C. Recognition and cleavage of DNA by a distamycin-salen·copper conjugate. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00299-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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43
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Park HJ, Kelly RC, Hurley LH. The Chemical Evolution of DNA−DNA Interstrand Cross-Linkers That Recognize Defined Mixed AT and GC Sequences. J Am Chem Soc 1996. [DOI: 10.1021/ja961678a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Hyun-Ju Park
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Robert C. Kelly
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
| | - Laurence H. Hurley
- Contribution from the Drug Dynamics Institute, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, and Pharmacia Upjohn Co., 301 Henrietta Street, Kalamazoo, Michigan 49001
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44
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Bell A, Kittler L, Löber G, Zimmer C. Influence of minor groove binders on the eukaryotic topoisomerase II cleavage reaction with 41 base pair model oligonucleotides. Invest New Drugs 1995; 13:271-84. [PMID: 8824345 DOI: 10.1007/bf00873133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This report deals with the cleavage reaction of calf thymus (CT) topoisomerase II with oligonucleotides containing one main cleavage site and adjacent binding sites for minor groove binders. The sequences of the oligonucleotides were derived from a pBR 322 sequence, which contains one main topoisomerase II cleavage site. The cleavage reaction was performed under increasing concentrations of minor groove binders and it showed characteristic inhibition dependences of topoisomerase II to the binding sites and to the binding length of the minor groove binders. The extension of the minor groove binder length on DNA from 4 to 10 base pairs (bp) by netropsin and bis-netropsin, respectively, causes a strong increase of the topoisomerase II cleavage inhibition. The same is observed by the introduction of a second minor groove binder sequence symmetrically positioned around the topoisomerase II main cleavage site. The combination of two different minor groove binders can lead to an increased topoisomerase II inhibition but also to a prevention of total inhibition as shown with chromomycin A3 and distamycin A at concentrations of 0.1 and 0.25 microM, respectively.
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Affiliation(s)
- A Bell
- Institut für Molekulare Biotechnologie e.V., Jena, Germany
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