Non-Covalent DNA-Binding Ruthenium Anticancer Drugs Anna Łęczkowska A thesis submitted to the University of Birmingham for the degree of Doctor of Philosophy School of Chemistry College of Engineering and Physical Sciences The University of Birmingham June 2011 I University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ACKNOWLEDGMENTS I would like to express my deep gratitude to all the people who provided me with their help and support during my PhD. I would like to acknowledge Prof. Mike Hannon for having me in his group and giving me many great opportunities to participate in a number of conferences and scientific events. Prof. Kevin Chipman, Dr. Chris Bunce and Dr. Nik Hodges and their groups and all those with whom I shared time in Biosciences laboratories are very gratefully acknowledged, especially Dr. Farhat Khanim for giving me much useful advice for cell tests and biological studies. Many thanks are also due to Dr. Louise Male who solved the crystal structures of my compounds, Dr. Neil Spencer for his help with NMR experiments and Peter Ashton for mass spectrometry. The work presented in this thesis was financially supported by the European Union (Marie Curie Fellowship, COST D39) and the University of Birmingham and to these institutions I would like to express my gratitude for the generous funding I obtained. Finally, I would like to thank to my family and friends. Without your love and support I would not be even half way through this journey. In particular, I am grateful to Jean-Louis. Thank you for everything you have done for me. II TABLE OF CONTENTS ABBREVIATIONS ……………………………………………………………….. vi ABSTRACT……..………………………………………………………………... x 1. Introduction 2 1.1 DNA structure and properties……………………………………………… 3 1.1.1 B-DNA structure…………………………………………………………. 3 1.2 Metallo-anticancer drugs………………………………………………….... 5 1.2.1 Cisplatin and its derivatives…………………………………………….. 6 1.2.2 Non-platinum antitumor agents………………………………………… 10 1.2.3 Ruthenium anticancer drugs……………………………………………. 10 1.3 Supramolecular DNA-binding anticancer drugs…………………….……. 15 1.3.1 Thermodynamics of drug-DNA interactions………………………...… 16 1.3.2 Metallointercalators and metalloinsertors…………………………….. 20 1.3.3 Binding to sugar phosphate backbone……………………………....... 27 1.3.4 Beyond the canonical right-handed double helix…………………….. 28 1.3.4.1 DNA junction structures recognition…………………………………. 29 1.3.4.2 G-quadruplex DNA recognition………………………………………. 30 1.4 Aim and outline of this thesis………………………………………………. 34 1.5 References…………………………………………………………………… 35 i 2. Dinuclear Ru(II) Triple-Stranded Helicates, Synthesis, DNA Binding 46 and Cytotoxic Activities 2.1 Introduction to supramolecular cylinders…………………………………. 47 2.2 Results and discussion……………………………………………………... 51 2.2.1 Synthesis of [Ru2L3]Cl4……………………………………………….... 51 2.2.2 Towards a library of ruthenium triple-stranded helicates………….... 55 o 2.2.3 Synthesis and characterisation of [Ru2L 3]Cl4…………………...…... 55 2-im 2.2.4 Synthesis and characterisation of [Ru2L 3]Cl4…………………….. 59 4(5)-im 2.2.5 Synthesis and characterisation of [Ru2L 3]Cl4…………………... 63 2.3 DNA binding studies………………………………………………………… 65 2.3.1 Circular dichroism………………………………………………………. 66 2.3.2 Linear dichroism……………………………………………………..….. 70 2.3.3 Agarose gel mobility shift assay………………………………………. 74 2.4 Cell viability assay…………………………………………………………… 77 2.5 General discussion, conclusions and further work………………………. 79 2.6 References…………………………………………………………………… 81 3. Optical Isomers of Ru(II) Triple-Stranded Helicate 84 3.1 Introduction…………………………………………………………………... 85 3.2 Results and discussion……………………………………………………... 88 3.2.1 Enantiomer separation…………………………………………………. 88 3.2.2 X-ray structure…………………………………………………………... 91 3.3 DNA binding studies……………………..………………………………….. 92 3.3.1 Flow linear dichroism spectroscopy…………………………………... 92 ii 3.3.2 Fluorescence response……………………………………………...…. 95 3.3.3 Agarose gel mobility shift assay………………………………………. 98 3.4 General discussion, conclusions and further work………………………. 100 3.5 References…………………………………………………………………… 104 4. The Enantiodifferentiation of Chiral Ruthenium(II) Triple-Stranded 106 Helicates by Δ-TRISPHAT 4.1 Introduction…………………………………………………………………... 107 4.2 Results and discussion……………………………………………………... 110 4.3 General discussion, conclusions and further work………………………. 115 4.4 References…………………………………………………………………… 118 5. Synthesis, Characterisation and DNA Binding Studies of Ru(II) 120 Complexes with Ammine and Azopyridyl Building Units 5.1 Introduction…………………………………………………………………... 121 5.2 Results and discussion……………………………………………………... 125 5.2.1 Synthesis……………………………………….................................... 125 a 5.2.1.1 Synthesis and characterisation of [Ru2L (NH3)8]Cl4………………. 125 a 5.2.1.2 Synthesis and characterisation of [RuL (NH3)4]Cl2……………...... 129 azpy 5.2.1.3 Synthesis and characterisation of [RuL (NH3)4]Cl2……………. 131 5.2.2 Interaction with DNA……………………………………………………. 134 5.2.2.1 Absorption spectral studies………………………………………….. 135 5.2.2.2 Circular dichroism…………………………………………………….. 136 5.2.2.3 Flow linear dichroism…………………………………………………. 137 iii 5.2.2.4 DNA thermal denaturation…………………………………………… 139 5.2.2.5 Agarose gel electrophoretic mobility shift assay………………….. 141 5.2.3 Cell tests…………………………………………………………………. 141 5.3 General discussion, conclusions and further work………………………. 142 5.4 References…………………………………………………………………… 143 6. Experimental 145 6.1 General……………………………………………………………………….. 146 6.2 Synthesis……………………………………………………………………... 146 6.2.1 Synthesis of cis-[Ru(DMSO)4Cl2]……………………………………… 146 6.2.2 Synthesis of L…………………………………………………………… 147 6.2.3 Synthesis of [Ru2L3]Cl4…………………………………………………. 148 6.2.3.1 Separation of optical isomers of [Ru2L3]Cl4………………………... 150 o 6.2.4 Synthesis of L .................................................................................. 151 o 6.2.5 Synthesis of [Ru2L 3]Cl4………………………………………………... 152 2-im 6.2.6 Synthesis of L .............................................................................. 154 2-im 6.2.7 Synthesis of [Ru2L 3]Cl4……………………………………………… 155 4(5)-im 6.2.8 Synthesis of L ............................................................................ 156 4(5)-im 6.2.9 Synthesis of [Ru2L 3]Cl4…………………………………………… 157 ox 6.2.10 Synthesis of L ………………………………………………………... 158 1 6.2.11 Synthesis of L ................................................................................ 159 2 6.2.12 Synthesis of L ………………………………………………………... 160 a 6.2.13 Synthesis of L …………………………………………………………. 161 a 6.2.14 Synthesis of [Ru2L (NH3)8]Cl4………………………………………... 162 iv a 6.2.15 Synthesis of [RuL (NH3)4]Cl2…………………………………………. 163 azpy 6.2.16 Synthesis of (E)-2-(phenyldiazenyl)pyridine, L …………………. 164 azpy 6.2.17 Synthesis of [RuL (NH3)4]Cl2……………………………………… 165 6.3 DNA binding studies………………………………………………………… 167 6.3.1 Materials and methods……………………………………………….… 167 6.3.2 Circular and linear dichroism…………………………………………... 168 6.3.3 Agarose gel experiments………………………………………………. 169 6.3.4 Thermal denaturation…………………………………………………… 169 6.4 Cell tests……………………………………………………………………… 170 6.5 References…………………………………………………………………… 171 7. Conclusions and Future Perspectives 172 v ABBREVIATIONS General abbreviations Å Angstrom aq. aqueous bpy 2,2’-bipyridine CH3CN acetonitrile CHCl3 chloroform DCM dichloromethane DSC Differential Scanning Calorimetry DMSO dimethyl sulphoxide DNA 2’-deoxyribonucleic acid EA Elemental Analysis EtOH ethanol ICP-MS Inductively Coupled Plasma Mass Spectrometry ITC Isothermal Titration Calorimetry M molar Me methyl MeOH methanol MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide NH4PF6 ammonium hexafluorophosphate t-Bu4NCl tetrabutylammonium chloride µM micromolar µmol micromole mmol millimole vi mp. melting point m/z mass/charge nm nanometer P partition coefficient Ph phenyl phen 1,10-phenanthroline RNA ribonucleic acid Tm melting temperature (ct-DNA) terpy 2,2’:6’,2’-terpyridine Spectroscopic terms CD Circular Dichroism LD Linear Dichroism ICD Induced Circular Dichroism IR Infra-Red NMR Nuclear Magnetic Resonance UV-Vis Ultra-Violet - Visible ES Electrospray MS Mass Spectrometry NMR terms CDCl3 deuterated chloroform CD3CN deuterated acetonitrile COSY Correlated Spectroscopy D2O deuterium oxide vii δ chemical shift d doublet dd doublet of doublets MHz megahertz ppm parts per million q quartet s singlet t triplet UV-Vis terms MLCT Metal to Ligand Charge Transfer ε extinction coefficient hv light energy λ wavelength Fluorescence terms λex Wavelength of excitation λem Wavelength of emission Thermodynamic terms ΔCp heat capacity change ΔG free energy change ΔH enthalpy change ΔS entropy change ΔT temperature change viii K equilibrium binding constant R gas constant (8.314 J K-1 mol-1) DNA terms ct-DNA calf-thymus DNA ds-DNA double-stranded DNA ss-DNA single-stranded DNA A adenine C cytosine G guanine T thymine 3WJ DNA three-way junction Gel electrophoresis terms ϕ unwinding angle σ superhelicity rb coalescence point ix ABSTRACT The research work described in this thesis concerns metal-based