Exploring the synthetic possibilities and siRNA delivery potential of Small Molecule Carriers (SMoCs) by Matthew John Gooding Submitted in accordance with the requirements for the degree of Doctor of Philosophy AUGUST 2011 UCL I, Matthew John Gooding, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. ___________________________________________________ 1 Abstract Delivery of proteins and nucleic acids into cells is a major challenge to the development of biological therapeutics. Cell penetrating peptides (CPPs) and cationic liposomes have been shown to internalise short interfering RNA (siRNA) to achieve gene silencing, but no standard reagent exists which can safely deliver macromolecules both in vitro and in vivo. Small Molecule Carriers (SMoCs) are amphipathic α-helix mimetics displaying guanidine groups in order to mimic the structure of the CPP penetratin. Previously, SMoCs were shown to effectively deliver active proteins into cells. It is hypothesized that SMoCs may also be applied to the delivery of siRNA into cells in order to knockdown target genes. In addition, since cell surface binding is thought to be a crucial step in CPP internalisation, a new SMoC which optimises binding to proteoglycans may be more efficiently taken up. The aims of this thesis are to optimise the synthesis of the SMoCs in order to increase the quantity of product; to demonstrate that SMoCs may be used as siRNA delivery agents; and to design and synthesize a new SMoC which maximises siRNA uptake. The synthesis of SMoCs has been significantly enhanced, with the development of new reagents to improve the yields and cost of production. The electrostatic interactions of SMoCs with siRNA have been characterised, using NMR to examine a π-cation interaction which may contribute to anion binding, as well as determination of binding affinities using ITC and gel shift assays. Initial experiments using SMoC-siRNA complexes show significant mRNA knowdown which demonstrates the potential of SMoCs as siRNA delivery vectors. Finally, a new SMoC has been designed and synthesized which represents the first in a new class of dendritic SMoCs which are designed to maximise binding to the cell surface. This SMoC is also capable of delivering siRNA into cells, and may also be expanded by the addition of targeting peptides. 2 Table of Contents Abstract ........................................................................................................................ 2 Table of Contents ......................................................................................................... 3 List of Figures .............................................................................................................. 9 List of Schemes .......................................................................................................... 10 List of Tables.............................................................................................................. 11 List of Abbreviations.................................................................................................. 12 Acknowledgements .................................................................................................... 14 Chapter 1: Introduction .......................................................................................... 16 1.1. Macromolecular Therapeutics ......................................................................... 16 1.2. Cell Penetrating Peptides ................................................................................ 22 1.2.1. Uptake Mechanism .................................................................................. 23 1.2.1.1. Cell-surface binding .......................................................................... 24 1.2.1.2. Endosomal Escape ............................................................................ 27 1.3. RNA Interference ............................................................................................ 29 1.3.1. Mechanism ............................................................................................... 29 1.3.2. Delivery .................................................................................................... 32 1.3.2.1. Chemical Modifications .................................................................... 33 1.3.2.2. Liposomes and Lipoplexes ................................................................ 34 1.3.2.3. Cationic Polymers ............................................................................. 36 1.3.2.4. Cell Penetrating Peptides .................................................................. 38 1.3.2.5. Nanocarriers ...................................................................................... 48 1.4. SMoCs ............................................................................................................. 51 1.4.1. Synthesis .................................................................................................. 52 1.4.2. Translocation activity ............................................................................... 54 1.5. Thesis Overview.............................................................................................. 54 3 Chapter 2: Improving the synthetic route to the SMoCs ..................................... 58 2.1. Introduction ..................................................................................................... 58 2.2. Results ............................................................................................................. 60 2.2.1. Modifications to the synthetic route to 4G-SMoC ................................... 60 2.2.1.1. Use of PMC protecting group ........................................................... 60 2.2.1.2. Improving Suzuki-Miyaura coupling ................................................ 65 2.2.1.3. New Guanidinylation reagent ........................................................... 67 2.2.1.4. Linker nitrile reduction ..................................................................... 67 2.2.2. 4G-SMoC with meta linker ...................................................................... 69 2.2.2.1. Thioamide linker ............................................................................... 71 2.2.2.2. Acid Linker ....................................................................................... 75 2.2.3. 4G-SMoC disulfide-linked dimer ............................................................ 78 2.3. Discussion ....................................................................................................... 82 Chapter 3: Exploring the interactions of SMoCs with siRNA ............................. 87 3.1. Introduction ..................................................................................................... 87 3.1.1. The SMoC π-cation interaction ................................................................ 87 3.1.2. Characterisation of SMoC-siRNA complexes ......................................... 88 3.1.3. SMoC-mediated siRNA transfection ....................................................... 89 3.2. Results ............................................................................................................. 93 3.2.1. Molecular Dynamics ................................................................................ 93 3.2.2. NMR pKa study ........................................................................................ 95 3.2.3. 6G-SMoC Synthesis ............................................................................... 102 3.2.4. ITC ......................................................................................................... 105 3.2.5. Gel Shifts ................................................................................................ 106 3.2.6. siRNA transfection ................................................................................. 109 3.3. Discussion ..................................................................................................... 112 4 Chapter 4: Designing a new SMoC for siRNA delivery ..................................... 117 4.1. Introduction ................................................................................................... 117 4.2. Results ........................................................................................................... 119 4.2.1. Design of a new SMoC analogue ........................................................... 119 4.2.2. 4G-SMoC-Dr synthesis .......................................................................... 122 4.2.3. Conjugation to RGD .............................................................................. 125 4.2.4. Gel Shift ................................................................................................. 128 4.2.5. PCR ........................................................................................................ 130 4.3. Conclusions ................................................................................................... 131 Chapter 5: Experimental Methods ....................................................................... 134 5.1. General Methods ........................................................................................... 134 5.1.1. General chemistry methods .................................................................... 134 5.1.2. Gel shifts ...............................................................................................