1
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Novel triazole and morpholine substituted bisnaphthalimide: Synthesis, photophysical and G-quadruplex binding properties. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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2
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Rad JA, Jarrahpour A, Aseman MD, Nabavizadeh M, Pournejati R, Karbalaei‐Heidari HR, Turos E. Design, Synthesis, DNA Binding, Cytotoxicity, and Molecular Docking Studies of Amonafide‐Linked
β
‐Lactam. ChemistrySelect 2019. [DOI: 10.1002/slct.201803785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Javad Ameri Rad
- Department of ChemistryCollege of SciencesShiraz University Shiraz 71946–84795 Iran
| | - Aliasghar Jarrahpour
- Department of ChemistryCollege of SciencesShiraz University Shiraz 71946–84795 Iran
| | | | - Masoud Nabavizadeh
- Department of ChemistryCollege of SciencesShiraz University Shiraz 71946–84795 Iran
| | - Roya Pournejati
- Molecular Biotechnology Lab.Department of Biology, Faculty of SciencesShiraz University Shiraz 71454 Iran
| | | | - Edward Turos
- Department of ChemistryUniversity of South Florida 4202 E. Fowler Avenue CHE 205 Tampa, FL USA
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3
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Jolley EA, Hardebeck LKE, Ren Y, Adams MS, Lewis M, Znosko BM. The effects of varying the substituent and DNA sequence on the stability of 4-substituted DNA-naphthalimide complexes. Biophys Chem 2018; 239:29-37. [PMID: 29804029 DOI: 10.1016/j.bpc.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/22/2018] [Accepted: 04/26/2018] [Indexed: 11/30/2022]
Abstract
DNA duplexes are stabilized by many interactions, one of which is stacking interactions between the nucleic acid bases. These interactions are useful for designing small molecules that bind to DNA. Naphthalimide intercalators have been shown to be valuable anti-cancer agents that stack between the DNA bases and exhibit stabilizing effects. There is a continued need to design intercalators that will exhibit these stabilizing effects while being more selective toward DNA binding. This work investigates 4-substituted naphthalimides with varying functional groups and their interactions with nucleic acid duplexes. Mode of binding was determined via wavelength scans, circular dichroism, and viscosity measurements. Optical melting experiments were used to measure the absorbance of the sample as a function of temperature. The Tm values derived from the DNA duplexes were subtracted from the Tm values derived from the DNA-intercalator complexes, resulting in ΔTm values. The ΔTm values demonstrated that the substituents on the intercalator affect the stability of the DNA-intercalator complex. From the results of this study and comparison to results from previous work, we conclude that the substituent type and position on the core intercalator molecule affect the stability of the complex it forms with DNA.
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Affiliation(s)
- Elizabeth A Jolley
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Laura K E Hardebeck
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Yi Ren
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Miranda S Adams
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Michael Lewis
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States
| | - Brent M Znosko
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103, United States.
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4
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Effect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes. Bioorg Med Chem 2015; 23:3586-91. [PMID: 25960324 DOI: 10.1016/j.bmc.2015.04.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/30/2015] [Accepted: 04/09/2015] [Indexed: 01/02/2023]
Abstract
DNA intercalators are commonly used as anti-cancer and anti-tumor agents. As a result, it is imperative to understand how changes in intercalator structure affect binding affinity to DNA. Amonafide and mitonafide, two naphthalimide derivatives that are active against HeLa and KB cells in vitro, were previously shown to intercalate into DNA. Here, a systematic study was undertaken to change the 3-substituent on the aromatic intercalator 1,8-naphthalimide to determine how 11 different functional groups with a variety of physical and electronic properties affect binding of the naphthalimide to DNA and RNA duplexes of different sequence compositions and lengths. Wavelength scans, NMR titrations, and circular dichroism were used to investigate the binding mode of 1,8-naphthalimide derivatives to short synthetic DNA. Optical melting experiments were used to measure the change in melting temperature of the DNA and RNA duplexes due to intercalation, which ranged from 0 to 19.4°C. Thermal stabilities were affected by changing the substituent, and several patterns and idiosyncrasies were identified. By systematically varying the 3-substituent, the binding strength of the same derivative to various DNA and RNA duplexes was compared. The binding strength of different derivatives to the same DNA and RNA sequences was also compared. The results of these comparisons shed light on the complexities of site specificity and binding strength in DNA-intercalator complexes. For example, the consequences of adding a 5'-TpG-3' or 5'-GpT-3' step to a duplex is dependent on the sequence composition of the duplex. When added to a poly-AT duplex, naphthalimide binding was enhanced by 5.6-11.5°C, but when added to a poly-GC duplex, naphthalimide binding was diminished by 3.2-6.9°C.
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5
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Hall JP, Cook D, Morte SR, McIntyre P, Buchner K, Beer H, Cardin DJ, Brazier JA, Winter G, Kelly JM, Cardin CJ. X-ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering. J Am Chem Soc 2013; 135:12652-9. [PMID: 23875832 DOI: 10.1021/ja403590e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz](2+) with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.
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Affiliation(s)
- James P Hall
- Chemistry Department, University of Reading, Whiteknights, Reading RG6 AD, United Kingdom
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6
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Banerjee S, Veale EB, Phelan CM, Murphy SA, Tocci GM, Gillespie LJ, Frimannsson DO, Kelly JM, Gunnlaugsson T. Recent advances in the development of 1,8-naphthalimide based DNA targeting binders, anticancer and fluorescent cellular imaging agents. Chem Soc Rev 2013; 42:1601-18. [DOI: 10.1039/c2cs35467e] [Citation(s) in RCA: 492] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Grzesiak W, Brycki B. Synthesis, FTIR, ¹³C-NMR and temperature-dependent ¹H-NMR characteristics of bis-naphthalimide derivatives. Molecules 2012; 17:12427-48. [PMID: 23090022 PMCID: PMC6268443 DOI: 10.3390/molecules171012427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/17/2012] [Accepted: 10/18/2012] [Indexed: 11/16/2022] Open
Abstract
Chemotherapy is still the most important method of cancer treatment. To make this method more effective and safe, new drugs to destroy cancer cells are needed. Some bis-naphthalimide derivatives show potential anticancer activity via an intercalation mechanism. A higher degree of DNA intercalation corresponds to better therapeutic effects. The degree of intercalation of naphthalimides depends on their structure, molecular dynamics and intermolecular interactions with DNA. In order to apply any active substance as a drug, its molecular dynamics as well as possible interactions with target molecules have to be examined in exhaustive details. This paper describes a practical preparation of some novel bis-naphthalimide derivatives with different functional groups and their FTIR and ¹H- and ¹³C-NMR spectral characteristics. To determine the molecular dynamics of the obtained compounds the temperature, their ¹H-NMR spectra were measured. It has been clearly proven in this paper that the unusual temperature-dependent ¹H-NMR behavior of the aromatic protons of phthalimide derivatives, previously described in the literature as "hypersensitivity" and explained by n-π interactions and molecular motions of aromatic amide rings, is a result of temperature driven changes of the geometry of carbonyl groups.
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Affiliation(s)
| | - Bogumił Brycki
- Author to whom correspondence should be addressed; ; Tel.: +48-61-829-1314; Fax: +48-61-829-1505
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8
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González-Bulnes L, Gallego J. Analysis of mixed DNA-bisnaphthalimide interactions involving groove association and intercalation with surface-based and solution methodologies. Biopolymers 2012; 97:974-87. [DOI: 10.1002/bip.22114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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9
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Tischer M, Pradel G, Ohlsen K, Holzgrabe U. Quaternary ammonium salts and their antimicrobial potential: targets or nonspecific interactions? ChemMedChem 2011; 7:22-31. [PMID: 22113995 DOI: 10.1002/cmdc.201100404] [Citation(s) in RCA: 213] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/28/2011] [Indexed: 11/07/2022]
Abstract
For more than 50 years dequalinium chloride has been used successfully as an antiseptic drug and disinfectant, particularly for clinical purposes. Given the success of dequalinium chloride, several series of mono- and bisquaternary ammonium compounds have been designed and reported to have improved antimicrobial activity. Furthermore, many of them exhibit high activity against mycobacteria and protozoa, especially against plasmodia. This review discusses the structure-activity relationships and the modes of action of the various series of (bis)quaternary ammonium compounds.
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Affiliation(s)
- Maximilian Tischer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
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10
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Ferri N, Radice T, Antonino M, Beccalli EM, Tinelli S, Zunino F, Corsini A, Pratesi G, Ragg EM, Gelmi ML, Contini A. Synthesis, structural, and biological evaluation of bis-heteroarylmaleimides and bis-heterofused imides. Bioorg Med Chem 2011; 19:5291-9. [PMID: 21880496 DOI: 10.1016/j.bmc.2011.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 07/28/2011] [Accepted: 08/09/2011] [Indexed: 11/18/2022]
Abstract
Bis-2,3-heteroarylmaleimides and polyheterocondensed imides joined through nitrogen atoms of the N,N'-bis(ethyl)-1,3-propanediamine linker were prepared from substituted maleic anhydrides and symmetrical diamines in good to satisfactory yields and short reaction times using microwave heating. The novel molecules were shown to inhibit proliferation of human tumor cells (NCI-H460 lung carcinoma) and rat aortic smooth muscle cells (SMCs) with variable potencies. Compound 11a, the most potent one of the series, showed IC(50) values comparable to those observed for the leading molecule elinafide in both cell lines, but with a higher selectivity toward human tumor cells. Compound 11a affected G1/S phase transition of the cell cycle, showed in vitro DNA intercalating activity and in vivo antitumor activity. A thorough structural analysis of the 11a-DNA complex was also made by mean of NMR and computational techniques.
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Affiliation(s)
- Nicola Ferri
- Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
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11
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Di Micco S, Mazué F, Daquino C, Spatafora C, Delmas D, Latruffe N, Tringali C, Riccio R, Bifulco G. Structural basis for the potential antitumour activity of DNA-interacting benzo[kl]xanthenelignans. Org Biomol Chem 2011; 9:701-10. [DOI: 10.1039/c0ob00480d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus. Antimicrob Agents Chemother 2010; 55:311-20. [PMID: 20937782 DOI: 10.1128/aac.00586-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Screening of various bisquaternary bisnaphthalimides against a variety of human pathogens revealed one compound, designated MT02, with strong inhibitory effects against Gram-positive bacteria. The MICs ranged from 0.31 μg/ml against community-acquired methicillin-resistant Staphylococcus aureus (MRSA) lineage USA300 to 20 μg/ml against Streptococcus pneumoniae. Radioactive whole-cell labeling experiments indicated a strong impact of MT02 on bacterial DNA replication. DNA microarray studies generated a transcriptional signature characterized by stronger expression of genes involved in DNA metabolism, DNA replication, SOS response, and transport of positively charged compounds. Furthermore, surface plasmon resonance and gel retardation experiments demonstrated direct binding of MT02 to DNA in a concentration-dependent, reversible, and non-sequence-specific manner. The data presented suggest that the bisquaternary bisnaphthalimide MT02 exerts anti-Gram-positive activity by binding to DNA and thereby preventing appropriate DNA replication.
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13
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Peixoto P, Bailly C, David-Cordonnier MH. Topoisomerase I-mediated DNA relaxation as a tool to study intercalation of small molecules into supercoiled DNA. Methods Mol Biol 2010; 613:235-56. [PMID: 19997888 DOI: 10.1007/978-1-60327-418-0_15] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Several biochemical and biophysical methods are available to study the intercalation of a small molecule between two consecutive base pairs of DNA. Among them, the topoisomerase I-mediated DNA relaxation assay has proved highly efficient, relatively easy to handle and very informative to investigate drug binding to DNA. The test relies on the use of a supercoiled plasmid to mimic the topological constraints of genomic DNA. The three main components of the assay - the topoisomerase I enzyme, DNA helix and intercalating small molecules - are presented here in a structural context. The principle of the assay is described in detail, along with a typical experimental protocol.
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Affiliation(s)
- Paul Peixoto
- INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Institut de Recherches sur le Cancer de Lille, Lille, France
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14
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Rettig M, Langel W, Kamal A, Weisz K. NMR structural studies on the covalent DNA binding of a pyrrolobenzodiazepine–naphthalimide conjugate. Org Biomol Chem 2010; 8:3179-87. [DOI: 10.1039/c001893g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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González-Bulnes L, Gallego J. Indirect Effects Modulating the Interaction between DNA and a Cytotoxic Bisnaphthalimide Reveal a Two-Step Binding Process. J Am Chem Soc 2009; 131:7781-91. [DOI: 10.1021/ja901505p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luis González-Bulnes
- Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain
| | - José Gallego
- Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain
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16
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Kumar TS, Madsen AS, Østergaard ME, Sau SP, Wengel J, Hrdlicka PJ. Functionalized 2'-amino-alpha-L-LNA: directed positioning of intercalators for DNA targeting. J Org Chem 2009; 74:1070-81. [PMID: 19108636 PMCID: PMC2853939 DOI: 10.1021/jo802037v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified oligonucleotides are increasingly applied in nucleic acid based therapeutics and diagnostics. LNA (locked nucleic acid) and its diastereomer alpha-L-LNA are two promising examples thereof that exhibit increased thermal and enzymatic stability. Herein, the synthesis, biophysical characterization, and molecular modeling of N2'-functionalized 2'-amino-alpha-L-LNA is described. Chemoselective N2'-functionalization of protected amino alcohol 1 followed by phosphitylation afforded a structurally varied set of target phosphoramidites, which were incorporated into oligodeoxyribonucleotides. Incorporation of pyrene-functionalized building blocks such as 2'-N-(pyren-1-yl)carbonyl-2'-amino-alpha-L-LNA (monomer X) led to extraordinary increases in thermal affinity of up to +19.5 degrees C per modification against DNA targets in particular. In contrast, incorporation of building blocks with small nonaromatic N2'-functionalities such as 2'-N-acetyl-2'-amino-alpha-L-LNA (monomer V) had detrimental effects on thermal affinity toward DNA/RNA complements with decreases of as much as -16.5 degrees C per modification. Extensive thermal DNA selectivity, favorable entropic contributions upon duplex formation, hybridization-induced bathochromic shifts of pyrene absorption maxima and increases in circular dichroism signal intensity, and molecular modeling studies suggest that pyrene-functionalized 2'-amino-alpha-L-LNA monomers W-Y having short linkers between the bicyclic skeleton and the pyrene moiety allow high-affinity hybridization with DNA complements and precise positioning of intercalators in nucleic acid duplexes. This rigorous positional control has been utilized for the development of probes for emerging therapeutic and diagnostic applications focusing on DNA targeting.
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Affiliation(s)
- T Santhosh Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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17
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Wilhelmsson LM, Kingi N, Bergman J. Interactions of Antiviral Indolo[2,3-b]quinoxaline Derivatives with DNA. J Med Chem 2008; 51:7744-50. [PMID: 19053744 DOI: 10.1021/jm800787b] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
| | - Ngarita Kingi
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
| | - Jan Bergman
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
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McMasters S, Kelly LA. Sequence-dependent interactions of cationic naphthalimides and polynucleotides. Photochem Photobiol 2007; 83:889-96. [PMID: 17645660 DOI: 10.1111/j.1751-1097.2007.00155.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding interactions of three naphthalimide derivatives with heteropoly nucleic acids have been evaluated using fluorescence, absorption and circular dichroism spectroscopies. Mono- and bifunctionalized naphthalimides exhibit sequence-dependent variations in their affinity toward DNA. The heteropoly nucleic acids, [Poly(dA-dT)]2 and [Poly(dG-dC)]2, as well as calf thymus (CT) DNA, were used to understand the factors that govern binding strength and selectivity. Sequence selectivity was addressed by determining the binding constants as a function of polynucleotide composition according to the noncooperative McGhee-von Hippel binding model. Binding affinities toward [poly(dA-dT)](2) were the largest for spermine-substituted naphthalimides (Kb = 2-6 x 10(6) M(-1)). The association constants for complex formation between the cationic naphthalimides and [poly(dG-dC)]2 or CT DNA (58% A-T content) were 2-500 times smaller, depending on the naphthalimide-polynucleotide pair. The binding modes were also assessed using a combination of induced circular dichroism and salt effects to determine whether the naphthalimides associate with DNA through intercalative, electrostatic or groove-binding. The results show that the monofunctionalized spermine and pyridinium-substituted naphthalimides associate with DNA through electrostatic interactions. In contrast, intercalative interactions are predominant in the complex formed between the bifunctionalized spermine compound and all of the polynucleotides.
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Affiliation(s)
- Sun McMasters
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore, MD, USA
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Ivanova A, Jezierski G, Vladimirov E, Rösch N. Structure of Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations. Biomacromolecules 2007; 8:3429-38. [PMID: 17894466 DOI: 10.1021/bm700549g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromophore-DNA complexes are useful for understanding charge transport along pi-stacks once their structural properties have been clarified. We studied two rhodamine 6G semicapping complexes with 15-mer B-DNA duplexes to determine the preferred orientation of the dye with respect to the neighboring base pair. For each of these systems, two distinct chromophore alignments were identified and quantified in terms of base-step parameters. The obtained geometries agree well with those derived from an NMR structure refinement of similar complexes. Cross-correlation analysis of the base-step parameters shows that slide and twist are highly interdependent during the structural transition from one conformation to the other.
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Affiliation(s)
- Anela Ivanova
- Department Chemie, Theoretische Chemie, Technische Universität München, Garching, Germany
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20
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Antonini I, Santoni G, Lucciarini R, Amantini C, Sparapani S, Magnano A. Synthesis and biological evaluation of new asymmetrical bisintercalators as potential antitumor drugs. J Med Chem 2007; 49:7198-207. [PMID: 17125272 DOI: 10.1021/jm0606793] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The good results obtained in the past decade with various types of potential bisintercalating agents, e.g., LU 79553, DMP 840, BisBFI, MCI3335, WMC-26, BisAC, BisPA, and the asymmetrical derivative WMC-79 (Chart 1), prompted us to investigate a new series of asymmetrical bisintercalators, compounds 1a-t (Chart 2), which can combine the potentiality of bisintercalation with a possible different mechanism of action due to two diverse chromophores. The DNA-binding properties of these compounds have been examined using fluorometric techniques: target compounds are excellent DNA ligands, with a clear preference for binding to AT-rich duplexes. In vitro cytotoxicity of these derivatives toward human hormone-refractory prostate adenocarcinoma cell line (PC-3) is described. Apoptosis assays of four selected compounds are also reported. Very potent cytotoxic compounds, some of them capable of inducing early apoptosis, have been identified.
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Affiliation(s)
- Ippolito Antonini
- Department of Chemical Sciences, University of Camerino, Via S. Agostino 1, Italy.
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21
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Chu Y, Sorey S, Hoffman DW, Iverson BL. Structural Characterization of a Rigidified Threading Bisintercalator. J Am Chem Soc 2007; 129:1304-11. [PMID: 17263414 DOI: 10.1021/ja066480x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NMR spectroscopy was used to explore the sequence-specific interaction of DNA with a new threading bisintercalator (C1) consisting of two intercalating 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) units connected by a rigid, tricyclic spiro linker. A structural model of C1 complexed to d(CGGTACCG)(2) was calculated using distance constraints obtained from solution NMR data. The model was also supported by the results from residual dipolar coupling (RDC) measurements obtained using Pf1-phage as a cosolvent. According to the model, the central cyclohexane ring of the linker connecting the two NDI units lies flat in the minor groove of DNA. Linker length, hydrogen bonding, steric, and hydrophobic factors all appear to contribute to the observed sequence specificity of binding. These results serve to illustrate the versatility of threading polyintercalation given that, in a previous study, a ligand consisiting of two NDI units joined by a flexible peptide linker was shown to bind sequence specifically within the major groove of this same sequence of DNA.
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Affiliation(s)
- Yongjun Chu
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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22
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Muth M, Hoerr V, Glaser M, Ponte-Sucre A, Moll H, Stich A, Holzgrabe U. Antitrypanosomal activity of quaternary naphthalimide derivatives. Bioorg Med Chem Lett 2007; 17:1590-3. [PMID: 17239596 DOI: 10.1016/j.bmcl.2006.12.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 12/21/2006] [Accepted: 12/26/2006] [Indexed: 10/23/2022]
Abstract
Sleeping sickness caused by Trypanosoma brucei gambiense and rhodesiense is fatal if left untreated. Due to the toxicity of drugs currently used and the emerging resistance against these drugs new lead compounds are urgently needed. Within the frame of a broad screening program for drugs with antitrypanosomal activity, some highly potent tertiary and quaternary mono- and bisnaphthalimides being active in the lower micromolar and nanomolar range of concentration have been identified. These compounds are easily available via a two- or three-step microwave-driven synthesis with high yield.
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Affiliation(s)
- Mathias Muth
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany
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Wamberg M, Walczak K, Andersen L, Hassan A, Pedersen E. Intercalating Nucleic Acids Containing Insertions of Naphthalimide. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690177] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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24
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25
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Woodhouse SL, Ziolkowski EJ, Rendina LM. Synthesis and anti-cancer activity of dinuclear platinum(ii) complexes containing bis(thioalkyl)dicarba-closo-dodecaborane(12) ligands. Dalton Trans 2005:2827-9. [PMID: 16094469 DOI: 10.1039/b508340k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel, dinuclear (2,2':6',2''-terpyridine)platinum(ii) complexes containing bis(thioalkyl)-dicarba-closo-dodecaborane(12)(carborane) ligands were prepared and characterised, and their preliminary anti-cancer characteristics have been determined in vitro; the complexes are the first examples of bis-intercalator complexes containing a boron-rich carborane cage.
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Affiliation(s)
- Susan L Woodhouse
- School of Chemistry and Physics, The University of Adelaide, Adelaide, South Australia 5005, Australia
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26
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Dance AM, Ralton L, Fuller Z, Milne L, Duthie S, Bestwick CS, Lin PKT. Synthesis and biological activities of bisnaphthalimido polyamines derivatives: cytotoxicity, DNA binding, DNA damage and drug localization in breast cancer MCF 7 cells. Biochem Pharmacol 2005; 69:19-27. [PMID: 15588710 DOI: 10.1016/j.bcp.2004.09.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Accepted: 09/08/2004] [Indexed: 11/26/2022]
Abstract
New bisoxynaphthalimidopolyamines (BNIPOPut, BNIPOSpd and BNIPOSpm) were synthesized. Their cytotoxic properties were evaluated against breast cancer MCF 7 cells and compared with bisnaphthalimidopolyamines BNIPSpd and BNIPSpm. Among the bisoxynaphthalimido polyamines, BNIPOSpm and BNIPOSpd exhibited cytotoxic activity with an IC50 f 29.55 and 27.22 microM, respectively, while BNIPOPut failed to exert significant cytotoxicity after 48-h drug exposure. DNA binding was determined by midpoint of thermal denaturation (Tm) measurement, ethidium bromide displacement and DNA gel mobility. Both BNIPOSpm and BNIPOSpd exhibited strong binding affinities with DNA. BNIPOPut had the least effect. The results were compared with other cytotoxic bisnaphthalimido compounds (BNIPSpm and BNIPSpd) previously reported by us. Using the single cell gel electrophoresis assay, it was found that BNIPSpm and BNIPSpd caused substantial DNA damage to MCF 7 treated cells while BNIPOSpm showed no significant effect over a range of drug concentrations after 4-h drug exposure. However, after 12-h drug exposure, BNIPOSpm had induced significant DNA damage similar to that of BNIPSpm (after 4-h drug exposure). Fluorescence microscopic analysis revealed that at 1 microM drug concentration and after 6-h drug exposure, both BNIPSpm and BNIPSpd were located within the cell while the presence of BNIPOSpm, was not observed. Therefore, we conclude that BNIPSpd, BNIPSpm and BNIPOSpm induce DNA damage consistent with their rate of uptake into the cells.
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Affiliation(s)
- Anne-Marie Dance
- The Robert Gordon University, School of Life Sciences, St. Andrew Street, Aberdeen AB251HG, Scotland, UK
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27
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Dai J, Punchihewa C, Mistry P, Ooi AT, Yang D. Novel DNA bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug. J Biol Chem 2004; 279:46096-103. [PMID: 15317822 DOI: 10.1074/jbc.m404053200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The new bisphenazine anticancer drug MLN944 is a novel cytotoxic agent with exceptional anti-tumor activity against a range of human and murine tumor models both in vitro and in vivo. MLN944 has recently entered Phase I clinical trials. Despite the structural similarity with its parent monophenazine carboxamide and acridine carboxamide anticancer compounds, MLN944 appears to work by a distinct mechanism of inhibiting DNA transcription rather than the expected mechanism of topoisomerase I and II inhibition. Here we present the first NMR structure of MLN944 complexed with d(ATGCAT)(2) DNA duplex, demonstrating a novel binding mode in which the two phenazine rings bis-intercalate at the 5'-TpG site, with the carboxamide amino linker lying in the major groove of DNA. The MLN944 molecule adopts a significantly unexpected conformation and side chain orientation in the DNA complex, with the N10 on the phenazine ring protonated at pH 7. The phenazine chromophore of MLN944 is very well stacked with the flanking DNA base pairs using the parallel base-stacking intercalation binding mode. The DNA sequence specificity and the groove recognition of MLN944 binding is determined by several site-specific hydrogen bond interactions with the central G:C base pair as well as the favorable stacking interactions with the 5'-flanking thymine. The specific binding site of MLN944 is known to be recognized by a number of important transcription factors. Our electrophoretic gel mobility shift assay results demonstrated that the c-Jun DNA binding to the AP-1 site is significantly inhibited by MLN944 in a dose-dependent manner. Thus, the exceptional biological activity of MLN944 may be due to its novel DNA binding mode leading to a unique mechanism of action.
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Affiliation(s)
- Jixun Dai
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, USA
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28
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Gallego J. Sequence-dependent nucleotide dynamics revealed by intercalated ring rotation in DNA-bisnaphthalimide complexes. Nucleic Acids Res 2004; 32:3607-14. [PMID: 15240833 PMCID: PMC484180 DOI: 10.1093/nar/gkh693] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bisnaphthalimide intercalators are anti-tumour agents composed of two planar rings linked by a flexible diazanonylene chain. The intercalated rings of three bisnaphthalimide analogues complexed to DNA are found here to undergo 180 degrees rotating motions that do not affect the diazanonylene linker atoms bound to the major groove. These ring rotations are detected by NMR spectroscopy in a broad range of sequence contexts and duplex lengths. A comparative analysis of the frequency and activation energies of such excited states in different complexes and conditions indicates that these motions (i) are unrelated to drug dissociation; (ii) are a consequence of concerted, sequence-dependent nucleotide movements taking place on the millisecond time scale; and (iii) may occur inside the DNA duplexes. The rotation frequencies range from 2 to 25 s(-1) at 25 degrees C, depending on DNA composition and the size of the rotating rings. The detected nucleotide dynamics are likely to play an important role in the binding kinetics of the numerous proteins and drugs that require base unstacking when interacting with DNA.
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Affiliation(s)
- José Gallego
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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29
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Braña MF, Cacho M, García MA, de Pascual-Teresa B, Ramos A, Domínguez MT, Pozuelo JM, Abradelo C, Rey-Stolle MF, Yuste M, Báñez-Coronel M, Lacal JC. New Analogues of Amonafide and Elinafide, Containing Aromatic Heterocycles: Synthesis, Antitumor Activity, Molecular Modeling, and DNA Binding Properties. J Med Chem 2004; 47:1391-9. [PMID: 14998328 DOI: 10.1021/jm0308850] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amonafide- and elinafide-related mono and bisintercalators, modified by the introduction of a pi-excedent furan or thiophene ring fused to the naphthalimide moiety, have been synthesized. These compounds have shown an interesting antitumor profile. The best compound, 9, was 2.5-fold more potent than elinafide against human colon carcinoma cells (HT-29). Molecular dynamic simulations and physicochemical experiments have demonstrated that these compounds are capable of forming stable DNA complexes. These results, together with those previously reported by us for imidazo- and pyrazinonaphthalimide analogues, have prompted us to propose that the DNA binding process does not depend on the electronic nature of the fused heterocycle.
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Affiliation(s)
- Miguel F Braña
- Departamentos de Ciencias Químicas, Facultad de Ciencias Experimentales y de la Salud, Universidad San Pablo CEU, Urbanización Montepríncipe, 28668-Boadilla del Monte, Madrid, Spain.
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30
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Zhang† W, Qian X, Wu Y, Ohrui H. A NEW CLASS OF DNA INTERCALATOR AND PHOTOCLEAVER: BIS-NAPHTHALIMIDES WITH BROMO AND NITRO SUBSTITUENTS. HETEROCYCL COMMUN 2003. [DOI: 10.1515/hc.2003.9.3.229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Braña MF, Cacho M, García MA, de Pascual-Teresa B, Ramos A, Acero N, Llinares F, Muñoz-Mingarro D, Abradelo C, Rey-Stolle MF, Yuste M. Synthesis, antitumor activity, molecular modeling, and DNA binding properties of a new series of imidazonaphthalimides. J Med Chem 2002; 45:5813-6. [PMID: 12477366 DOI: 10.1021/jm020950q] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of mono and bisintercalators based on the 5,8-dihydrobenz[de]imidazo[4,5-g]isoquinoline-4,6-dione system were synthesized and evaluated for growth inhibitory properties in several human cell lines. All target compounds showed activity in the micromolar range. Representative compounds were evaluated using UV--vis spectroscopy and viscosimetric determinations, showing that they behave as DNA intercalators. Molecular modeling techniques were used in order to rationalize the moderate activity observed for bisnaphthalimides.
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Affiliation(s)
- Miguel F Braña
- Departamentos de Química Orgánica y Farmacéutica, Facultad de Ciencias Experimentales y de la Salud, Universidad San Pablo CEU, Urbanización Montepríncipe, 28668-Boadilla del Monte, Madrid, Spain.
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32
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Ikeda H, Nakamura Y, Saito I. Synthesis and characterization of naphthalimide-containing peptide nucleic acid. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01164-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Abstract
Recent years have seen considerable progress in simulations of nucleic acids. Improvements in force fields, simulation techniques and protocols, and increasing computer power have all contributed to making nanosecond-scale simulations of both DNA and RNA commonplace. The results are already helping to explain how nucleic acids respond to their environment and to their base sequence and to reveal the factors underlying recognition processes by probing biologically important nucleic acid-protein interactions and medically important nucleic acid-drug complexation. This Account summarizes methodological progress and applications of molecular dynamics to nucleic acids over the past few years and tries to identify remaining challenges.
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Affiliation(s)
- Emmanuel Giudice
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris 75005, France
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34
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Guelev V, Sorey S, Hoffman DW, Iverson BL. Changing DNA grooves--a 1,4,5,8-naphthalene tetracarboxylic diimide bis-intercalator with the linker (beta-Ala)(3)-Lys in the minor groove. J Am Chem Soc 2002; 124:2864-5. [PMID: 11902864 DOI: 10.1021/ja016834e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have been investigating a modular, threading DNA polyintercalator design based upon the 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit. Previously, we have reported the NMR analysis of a bis-intercalator-DNA complex in which the peptide linker between NDI units was found to occupy the DNA major groove (Guelev, Lee, Sorey, Hoffman, Iverson, Chem. Biol. 2001, 8, 415-425). Here we describe the NMR analysis of a complex between a related bis-intercalator known to display altered DNA sequence specificity. In this case, the linker resides in the DNA minor groove. We have thus shown that within this set of sequence specific bis-intercalators, both DNA grooves can be accessed, setting the stage for longer threading polyintercalators designed to have linkers occupying both grooves in an alternating fashion.
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Affiliation(s)
- Vladimir Guelev
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78722, USA
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35
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Owen EA, Burley GA, Carver JA, Wickham G, Keniry MA. Structural investigation of the hedamycin:d(ACCGGT)2 complex by NMR and restrained molecular dynamics. Biochem Biophys Res Commun 2002; 290:1602-8. [PMID: 11820806 DOI: 10.1006/bbrc.2002.6369] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hedamycin, a member of the pluramycin family of drugs, displays a range of biological responses including antitumor and antimicrobial activity. The mechanism of action is via direct interaction with DNA through intercalation between the bases of the oligonucleotide and alkylation of a guanine residue at 5'-PyG-3' sites. There appears to be some minor structural differences between two earlier studies on the interaction of hedamycin with 5'-PyG-3' sites. In this study, a high-resolution NMR analysis of the hedamycin:d(ACCGGT)2 complex was undertaken in order to investigate the effect of replacing the thymine with a guanine at the preferred 5'-CGT-3' site. The resultant structure was compared with earlier work, with particular emphasis placed on the drug conformation. The structure of the hedamycin:d(ACCGGT)2 complex has many features in common with the two previous NMR structures of hedamycin:DNA complexes but differed in the conformation and orientation of the N,N-dimethylvancosamine saccharide of hedamycin in one of these structures. The preferential binding of hedamycin to 5'-CG-3' over 5'-TG-3' binding sites is explained in terms of the orientation and location of the N,N-dimethylvancosamine saccharide in the minor groove.
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Affiliation(s)
- Elisabeth A Owen
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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36
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Spicer JA, Gamage SA, Finlay GJ, Denny WA. Synthesis and evaluation of unsymmetrical bis(arylcarboxamides) designed as topoisomerase-targeted anticancer drugs. Bioorg Med Chem 2002; 10:19-29. [PMID: 11738603 DOI: 10.1016/s0968-0896(01)00249-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Symmetrical dimers of lipophilic intercalating chromophores linked by cation-containing chains have recently been shown to have broad-spectrum in vivo anticancer activity. We report the preparation and evaluation of a series of both symmetric and unsymmetric dimers of a variety of intercalating chromophores of varied DNA binding strength, including naphthalimides, acridines, phenazines, oxanthrenes and 2-phenylquinolines. The unsymmetrical dimers were prepared by sequential coupling of the chromophores to linkers with selectively protected primary terminal amines to ensure high yields and unequivocal product. Protection of the internal (secondary) amines as BOC derivatives was used to ensure complete structural specificity, and was also an aid to the purification of these very polar compounds. The growth inhibitory abilities (as IC(50) values) of the compounds in a range of cell lines showed that the nature of the linker chain was important, and independent of the nature of the chromophore, with compounds containing the dicationic linker [-(CH2)2NH(CH2)2NH(CH2)2-] being on average 30-fold more potent than the corresponding compounds containing the monocationic linker [-(CH2)3NMe(CH2)3-]. However, the chromophores also play a role in determining biological activity, with the cytotoxicities of symmetric and unsymmetric dicationic dimers correlating with the overall DNA binding abilities of the chromophores.
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Affiliation(s)
- Julie A Spicer
- Auckland Cancer Society Research Centre, Faculty of Medical & Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1000, New Zealand.
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37
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Guelev VM, Cubberley MS, Murr MM, Lokey RS, Iverson BL. Design, synthesis, and characterization of polyintercalating ligands. Methods Enzymol 2001; 340:556-70. [PMID: 11494870 DOI: 10.1016/s0076-6879(01)40442-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- V M Guelev
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
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38
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Guelev V, Lee J, Ward J, Sorey S, Hoffman DW, Iverson BL. Peptide bis-intercalator binds DNA via threading mode with sequence specific contacts in the major groove. ACTA ACUST UNITED AC 2001; 8:415-25. [PMID: 11358689 DOI: 10.1016/s1074-5521(01)00013-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND We previously described a general class of DNA polyintercalators in which 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) intercalating units are connected via peptide linkers, resulting in the first known tetrakis- and octakis-intercalators. We showed further that changes in the composition of the peptide tether result in novel DNA binding site specificities. We now examine in detail the DNA binding mode and sequence specific recognition of Compound 1, an NDI bis-intercalator containing the peptide linker gly-gly-gly-lys. RESULTS 1H-NMR structural studies of Compound 1 bound to d(CGGTACCG)(2) confirmed a threading mode of intercalation, with four base pairs between the diimide units. The NMR data, combined with DNAse I footprinting of several analogs, suggest that specificity depends on a combination of steric and electrostatic contacts by the peptide linker in the floor of the major groove. CONCLUSIONS In view of the modular nature and facile synthesis of our NDI-based polyintercalators, such structural knowledge can be used to improve or alter the specificity of the compounds and design longer polyintercalators that recognize correspondingly longer DNA sequences with alternating access to both DNA grooves.
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Affiliation(s)
- V Guelev
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 78722, USA
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39
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Gamage SA, Spicer JA, Finlay GJ, Stewart AJ, Charlton P, Baguley BC, Denny WA. Dicationic bis(9-methylphenazine-1-carboxamides): relationships between biological activity and linker chain structure for a series of potent topoisomerase targeted anticancer drugs. J Med Chem 2001; 44:1407-15. [PMID: 11311063 DOI: 10.1021/jm0003283] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bis(9-methylphenazine-1-carboxamides) joined by a variety of dicationic (CH(2))(n)()NR(CH(2))(m)NR(CH(2))(n) linkers of varying length (carboxamide N-N distances from 11.0 to 18.4 A) and rigidity were prepared by reaction of 9-methylphenazine-1-carboxylic acid imidazolide with the appropriate polyamines. The compounds were evaluated for growth inhibitory properties in P388 leukemia, Lewis lung carcinoma, and wild-type (JL(C)) and mutant (JL(A) and JL(D)) forms of human Jurkat leukemia with low levels of topoisomerase II (topo II). The compounds all had IC(50) ratios of <1 in the resistant Jurkat lines, consistent with topo II inhibition not being the primary mechanism of action. Analogues joined by an (CH(2))(2)NR(CH(2))(2)NR(CH(2))(2) linker were extremely potent cytotoxins, with selectivity toward the human cell lines, but absolute potencies declined sharply from R = H through R = Me to R = Pr and Bu. In contrast, (CH(2))(2)NR(CH(2))(3)NR(CH(2))(2) compounds showed reverse effects, with the R = Me analogue being more potent than the R = H one as well as being the most potent in the series [IC(50) in JL(C) cells 0.08 nM; superior to that for the clinical bis(naphthalimide) LU 79553]. Overall, the IC(50)s of analogues with linker chains (CH(2))(n)NH(CH(2))(m)NH(CH(2))(n) were inversely proportional to linker length. Constraining the rigidity of the linker chain by incorporating a piperazine ring did not decrease potency significantly. A representative compound bound tightly to DNA with high selectivity for GC sites, compatible with recent work suggesting that compounds of this type place their side chains in the major groove, making specific contacts with guanine bases. Representative compounds were susceptible to transport mediated resistance, being much less effective in cells that overexpressed P-glycoprotein. Overall the results suggest these compounds have a similar mode of action, mediated primarily by poisoning of topo I (possibly with some involvement of topo II). The bis(9-methylphenazine-1-carboxamides) show very high in vitro growth inhibitory potencies compared to their monomeric analogues. Two compounds showed in vivo activity in murine colon 38 syngeneic and HT29 human colon tumor xenograft models using intraperitoneal dosing.
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Affiliation(s)
- S A Gamage
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1000, New Zealand
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40
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Onfelt B, Lincoln P, Nordén B. Enantioselective DNA threading dynamics by phenazine-linked. J Am Chem Soc 2001; 123:3630-7. [PMID: 11457094 DOI: 10.1021/ja003624d] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions between the stereoisomers of the chiral bis-intercalator [mu-C4(cpdppz)(2)-(phen)(4)Ru(2)](4+) and DNA reveal interesting dynamic discrimination properties. The two enantiomers Delta-Delta and Lambda-Lambda both form very strong complexes with calf thymus DNA with similar thermodynamic affinities. By contrast, they display considerable variations in their binding kinetics. The Delta-Delta enantiomer has higher affinity for calf thymus DNA than for [poly(dA-dT)](2), and the association kinetics of the dimer to DNA, as well as to polynucleotides, requires a multiexponential fitting function. The dissociation reaction, on the other hand, could be described by a single exponential for [poly(dA-dT)](2), whereas two exponentials were required for mixed-sequence DNA. To understand the key mechanistic steps of the reaction, the kinetics was studied at varied salt concentration for different choices of DNA and chirality of the threading complex. The enantiomers were found to have markedly different dissociation rates, the Lambda-Lambda enantiomer dissociating about an order of magnitude faster than the Delta-Delta enantiomer. Also, the salt dependence of the dissociation rate constants differed between the enantiomers, being stronger for the Lambda-Lambda enantiomer than for the Delta-Delta enantiomer. Since the dissociation reaction requires unthreading of bulky parts of the bis-intercalator through the DNA helix, a considerable conformational change of the DNA must be involved, possibly defining the rate-limiting step.
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Affiliation(s)
- B Onfelt
- Department of Physical Chemistry, Chalmers University of Technology, S-412 96 Gothenburg, Sweden
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