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Investigation of Fluorophore Motifs for Protease Detection

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Investigation of Fluorophore Motifs for Protease Detection INVESTIGATION OF FLUOROPHORE MOTIFS FOR PROTEASE DETECTION THESIS submitted for the degree of DOCTOR OF PHILOSOPHY in Chemistry at Kingston University London by Luke James Bywaters School of Life Sciences, Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston-upon-Thames, Surrey, KT1 2EE. December 2018 1 DECLARATION This thesis entitled Investigation of Fluorophore Motifs for Protease Detection is based upon work conducted by the author in the School of Life Sciences, Pharmacy and Chemistry at Kingston University London between October 2013 and May 2017. All of the work described herein is original unless otherwise acknowledged in the text or by references. None of the work has been submitted for another degree in this or any other universities. ___________________ Luke James Bywaters 2 “Where you arrive does not matter as much as what sort of person you are when you arrive there.” – Seneca 3 In Memory of My Mother Jan 4 Acknowledgments Acknowledgments First and foremost, I would like to thank my supervisor, mentor, and above all, friend Dr Adam Le Gresley, without whom there is not a chance that I would have survived long enough to reach this stage. Any words I could put to paper could not adequately describe the debt of gratitude I owe to him. He has provided me with constant support, guidance and an unwavering belief that I could get through this, especially when times were really tough. These characteristics in any person, in my opinion define a role model which we could, and should all aspire to. Secondly, I would like to thank Dr Alex Sinclair, who’s hard work and lobbying provided me with the opportunity to undertake this PhD project, may he enjoy the very best of fortunes in his new career path. I would also like to thank my friend Dr Jean-Marie Peron, the in house NMR ‘don’. Who not only helped me out with the intricacies of both NMR and synthetic methodology on countless occasions, but also provided a sounding board for my perpetual complaining, swearing and general bad manner! Not only did he put up with me, but was always full of much needed advice and banter to bring a smile to my face when I needed it, often in the pub after a hard day in the lab. I would also like to express my eternal gratitude to my friends Luke Stokes and Griff Williams, who were there in a flash when I really needed them, and continued to be there all through my troubled times. Without those guys and their support and faith in me, I don’t know where I would be today. They showed me what a true friend really is. It remains for me to thanks my colleagues and friends from the LeGresley Research lab: the legendary Paddy Melia, one of my best friends and a more than worthy sparring opponent, who’s banter I still bear the scars of! My friends Navid Shokri and Dr Rosa Busquets, who’s consistent advice and unwavering confidence in me, even when I was seriously lacking them myself helped me indescribably. My Friend and contemporary Samerah Malik, who always maintained confidence in me with unconditional kindness and good advice even when my own faculties failed me, but without sparing the odd kick up the derriere when suitably required! My friend Alex Fudger who provided a shoulder to lean on with consistent good advice which kept me on track throughout the hard times. Finally I would like to thank my lady Margarida, for her love, support, encouragement and for never giving up on me. She was always there to give me something to strive towards and look forward to, without which I couldn’t have got through this. Furthermore I would also like to thank her for putting up with me and all the associated hassle and heartache that entailed. If trophies were awarded for such things, a large cabinet would be in order to house her collection. All that remains is to thank Kingston University for providing the funding for this project, without which I am certain I could not have taken it on. 5 Abstract Abstract There is an increasing and serious problem of antimicrobial resistance emerging where previously useful antibiotics are no longer effective. This causes a significant monetary and human cost in the healthcare system, and is a direct result of the misuse and over prescription of antibiotics. The development and implementation of rapid point of care diagnostics to conclusively identify problem pathogens such as Staphylococcus aureus could slow the emergence of antibiotic resistance by correctly targeted antibiotic therapy. The rapid and sensitive protease detecting LGX probe is an example of such a diagnostic test. The synthesis of this rhodamine based fluorogenic probe and the investigation of other fluorescence motifs for protease detection has been the focus of this project. Scale up and optimisation of the synthetic route to the previously produced LGX probe was achieved, allowing further testing in a healthcare environment. Previous work has failed to address the complexities associated with the use of conventional fluorescence motifs for probe generation, as well as the ways in which their fluorescence may be modulated. Herein we address these problems, and those encountered with the scale up of the ‘LGX’ probe. The lessons learned from the LGX synthesis provided the basis for development of a number of novel analogues of the orphan fluorophore class Singapore Green. A library of nine simplified and highly active fluorescent Singapore Greens were generated. These were exhaustively investigated and it was determined how structural variations effect both their spectral and fluorescence properties including quantum yield and extinction coefficient. The spectral characteristics of Singapore Green fluorescent motifs were found to be highly favourable allowing them to provide the central core of future probes. This work has also provided the synthetic methodology required to produce ‘LGX’ in the quantities required for eventual utilisation in healthcare environments. Furthermore it has provided the several novel platforms for the development of future probes. This is of potentially considerable value as it may not only contribute to the reduction of the problem 6 Abstract pathogen S. aureus as well as slow the emergence of resistance, but also facilitate generation of other important protease detection systems. 7 Abbreviations Abbreviations ACE angiotensin-converting enzyme Arg arginine BIOPEP bioactive peptides Boc tertiary butoxycarbonyl BODIPY borondipyrrolmethine br broad CA coupling agent Cbz benzyloxycarbonyl COMU (1-cyano-2-ethoxy-2-oxoethylidenaminooxy)dimethylamino-morpholino- carbeniumhexafluorophosphate d doublet DCM dichloromethane δ chemical shift in parts per million dd doublet of doublets DDAO 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) DDQ 2,3-dichloro-5,6-dicyano-1,4-benzoquinone DIEA diisopropyl ethylamine DMF dimethyl formamide DMSO dimethyl sulfoxide DPP-4 dipeptidyl peptidase-4 EDCI 1-(3-dimethylaminopropyl)-3-ethylycarbodiimide hydrochloride EEDQ N-Ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline eq equivalent ESBL extended spectrum β - lactamases EtOAc ethyl acetate FP-2 Falcipain-2 HABP hospital acquired bacterial pneumonia HATU (1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium-3-oxid hexafluorophosphate HPLC high performance liquid chromatography HR MS high resolution mass spectrometry IR infra-red m multiplet 8 Abbreviations MAPKK mitogen-activated protein kinase kinase MDAP mass directed auto purification Me methyl MeOH methanol MRSA methicillin resistant Staphylococcus aureus MSSA methicillin sensitive Staphylococcus aureus m/z mass to charge ratio NMR nuclear magnetic resonance PCR polymerase chain reaction ppm parts per million Pro proline PRSP penicillin resistant Streptococcus pneumoniae PSMA prostate specific membrane antigen PyBOP (benzotriazole-1-ylxoy)tris(pyrrolidino)phosphonium hexafluorophosphate q quartet Rf retention factor Rho Rhodamine 110 ROI return on investment rt room temperature SNAP soluble N-ethylmaleimide-sensitive factor attachment protein SNARE soluble N-ethylmaleimide-sensitive factor attachment protein receptor TFA trifluoroacetic acid THF tetrahydrofuran TLC thin layer chromatography VABP ventilator acquired bacterial pneumonia Val valine VRE vancomycin resistant enterococci 9 Table of Contents Table of Contents 1. Chapter 1 - Introduction ............................................................................................ 19 1.1 Introduction to Proteases ........................................................................................ 20 1.1.1 Definition and Function ........................................................................................... 20 1.1.2 Organisation ........................................................................................................... 22 1.1.3 Aspartic Proteases .................................................................................................. 22 1.1.4 Cysteine Proteases ................................................................................................. 23 1.1.5 Serine Proteases .................................................................................................... 23 1.1.6 Metalloproteases..................................................................................................... 23 1.2 Protease Activity ...................................................................................................... 24 1.2.1 Accurate Antimicrobial Targeting via Protease Activity ............................................ 24 1.3 Protease Detection .................................................................................................
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