Durham University a Thesis Entitled the Development of Thiophosphoryl ^ Click' Chemistry

Durham E-Theses The development of thiophosphoryl 'click' chemistry Trmcic, Milena How to cite: Trmcic, Milena (2009) The development of thiophosphoryl 'click' chemistry, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/2035/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk Durham University A thesis entitled The Development of Thiophosphoryl ^ Click' Chemistry 'The copyright of this thesis rests-with-the author or the university to which it was submitted. No quotation from it, or information derived from it may be published without the prior written consent of the author or university, and any information derived from it should be Submitted by acknowledged. Milena Trmcic Department of Chemistry A Candidate for the Degree of Doctor of Philosophy 2009 0 1 SEP 2009 ACKNOWLEDGMENTS I would like to express my gratitude to my supervisor, Dr. David R W Hodgson, who enabled my PhD studies and has provided amazing support and supervision through entire project along v^th the great guidance in producing this thesis. In addition, I would also like to convey thanks to the Durham University Chemistry Department for providing the fmanciaj meaiis and the laboratory facilities This research project was performed with great help of the departmental excellent technical stuff in the form of NMR spectroscopy analysis by Dr. Alan Kenvvright, Mr Ian McKeag and Mrs Catherine Heffeman; mass spectroscopy analysis by Dr. Mile Jones, Dr. Jackie Mosely, and Miss Lara Turner; Mr Tony Baxter, Mrs Elizbeth Wood and Mr Philip Rochester in stores and glassblov^ng by Mr Peter Coyne and Mr Malcolm Richardson. I would like to thank Prof. "Robert Edwards and his group, especiailly to Dr. Ian Cummins, Dr. Mark Skipsey and Dr. David Dixon for generous and abundant help, advice in undertaking research, but also for fruitful chats and discussions. I would also like to thank the past and present members our ^oup for all assistance and creation of pleasant laboratory atmosphere. Very special thanks to my gorgeous nephew Luka Cvitas, my sister Jelena Trmcic Cvitas and brother-in-law Marko Cvitas for exceptional support in any means, great housting for my frequent visits and making my stay in Great Britain exceedingly enjoyable. Many thanks to my mum, father and, especially, brother Marko for all love and understanding. I would like to express big gratitude to my boyfriend, Igor Simovic, for endless love and patience through my stay abroad. Finally, I would like to thank to my friends back in Serbia and in Durham for all laughs, good food discussions, Sunday movie nights and support in studies, in particular to Anne Soleilhavoup whose friendship evaluation would lead to indefinite numbers. MEMORANDUM The work that is presented with in this thesis was carried out at Durham University between January 2006 and April 2009 The thesis is the work of the author, except where acknowledged by reference, and has not been submitted for any other degree. The copyright of these lies solely with the author and no quotation from it would be published from it should be published without written consent and information derived form it should be acknowledged. This work has been presented at: RSC Nucleic Acids Group, The 2"^ Nucleic Acids Forum, Bio-organic Chemistry and Biochemistry, July 2006, University of Manchester, Manchester, UK » RSC Organic Reaction Mechanisms Meeting, Post-Graduate Symposium, September 2006 GlaxoSmithKline, Tonbridge, UK • RSC Nucleic Acids Group, The S'** Nucleic Acids Foriim, Bio-organic Chemistry and Biochemistry, July 2007, University of Reading, Reading, UK = RSC Organic Reaction Mechanisms Group, 'Younger' Physical Organic Chemists' Residential Meeting, July 2007, Castelton, UK " RSC Organic Reaction Mechanisms Group, SymPoc 2008, Durham University, Durham, UK " 19* lUPAC Conference on Physical Organic Chemistry July 2008, The Royal University of Santiago de Compostela, Santiago de Compostela, Spain " RSC Organic Reaction Mechanisms Group, 'Younger' Physical Organic Chemists' residential Meeting, September 2008, Castelton, UK " 2"** EuChMS Chemsitry Congress, September 2008, Torino, Italy • RSC Organic Reaction Mechanisms Group, Post-Graduate Symposium, November 2008, AstraZeneca, Loughborough, UK STATEMENT OF COPYRIGHT No part of this thesis may be reproduced by any means, nor translated, hot transmitted into any machine language without written permission of the author. Ftir iLuka and iMarko: ACKNOWLEDGMENTS 1 ABSTRACT^ ^ 9 ABBREVIATIONS 10 1.0 INTRODUCTION 13 1.1. The 'Click' chemistry concept 14 1.1.1. Why water as the solvent? _ ^ 16 1.1.2. Some of examples of 'Click' chemistry ^ 17 1.1.3. Wide application in biological systems 22 1.2. Phosphates 26 1.3. Research targets in the form of glycosyltransferases 29 1.4. Nucleophilic reactions in water 31 1.4.1. The effect of the general base assisted hydrolysis on nucleophilic reactions in water 37 1.4.2. The phenomenon of high yields in the reactions of benzenesulfonyI chloride with amines at high pH^ 40 1.5. Project outline: Development of thiophosphoryl 'Click' chemistry 43 •1.5.1. Thiophosphoroamidate systdm .43 1.5.2. Bromoacetyl system 44 2.0 The Thiophosphoroamidate system 46 2.1. The foundation of the thiophosphoramidate idea 48 2.2. Simplification of the diphosphate motifs-development of mono S-alkylated thiophosphoramidates 51 2.3. Existing methods for generating thiophosphoramidates 53 2.4. Preliminai^ experiments: thiophosphorylation of amines 56 2.4.1. Thiophosphorylation of ethanolamine: optimisation 57 2.4.2. Thiophosphorylation of benzylamine 58 2.5. Hydrolysis stability studies on a thiophosphoramidate 61 2.5.1. Stability of oxy-phosphoroamidates 61 2.5.2. Stability of thiophosphoroamidates 64 2.5.3. NMR kinetic studies: ethanolamine thiophosphoramidate hydrolysis 68 2.6. Preliminary alkylation experiments: stepwise approach 76 2.6.1. The use of an excess of thiophospboroamidate 77 2.6.2. Bis-(N-, S-) alkylation of thiophosphoramidates 81 2.6.3. The use of equal numbers of equivalents of thiophosphoramidate and alkylating agent 82 2.7. Design of a one-pot thiophosphoramidate system 84 2.8. Model amines ^ , 86 2.9. Model alkylating agents^ 89 2.10. Continuous method with lipophilic amines and simple alkylating agents: benzylamine and allylamine 91 2.11. One-pot method with hydrophilic amines: the use of excess of thiophosphoryl chloride and methanol precipitation 95 2.12. Continuous method: the use of excess of morpholine 97 2.13. One-pot method: the use an equal number of equivalents of ethanolamine and thiophosphoryl chloride 99 2.14. Exploitation of the one-pot method: proof of concept generation of a library of amines 100 2.15. The stability of S-alkylated thiophosphoroamidates 103 2.16. 'ChaUenging' amines: amino acids, aromatic amines and sugars 105 2.16.1. The aqueous thiophosphorylation of phenylalanine 105 2.16.2. Continuous Tripartite method: aniline ^ 108 2.16 J. The aqueous thiophosphorylation of glucosamine , 109 2.17. Expansion to a range of alkylating agents 112 2.18. Conclusions on and potential of the thiophosphoroamidate system in future experiments 115 3.0 Nucleosides and their application in the thiophosphoramidate system 118 3.1. Research targets m the form of glycosyltransferases 120 3.1.1. Fucosyltransferase ^ 120 3.1.2. Past and present inhibitors: mimics of the natural substrate 122 3.2. Synthesis of guanosine derivatives 126 3.2.1. Preparation of 5'-iodo-5'-deoxyguanosine 126 3.2.2. Preparation of 5'-azido-5'-deoxyguanosine , 127 3.2.3. Novel aqueous procedure for the preparation of 5'-a3ddo-5'-deoxyguanosine** ^ - 127 3.2.4. Novel aqueous procedure for the preparation of S'-aniino-S'-deoxyguahosine''* 128 3.3. Continuous method involving nucleosides: 5'-amino-5'-deoxyguanosine 130 3.4. Continuoiis method involving nucleosides: 5'-amino-5'-deoxyadenosme 133 3.5. S'-Iodo-5'-deoxyguanosine as an alkylating agent , 134 3.6. Conclusions and future work on the involvement of nucleosides in the thiophosphoramidate system 137 4.0 Quinolines and their application in the thiophosphoramidate system ^ 139 4.1. A simple opportunity for the application of the thiophosphoramidate system: quinoline-based thiophosphoramidates as antileishmanials 140 4.2. Leishmaniasis, past and present drugs . _ , 141 4.3. Library synthesis and analysis ^ ^ 142 4.4. Biological testing against Leishmania mexicana 144 4.4.1. Initial screening 144 4.4.2. Estimation of the ICgoS of the studied quinoline compounds 144 4.5. Hypothesis 148 4.6. Conclusions and future work on quinoline-based thiophosphoramidates 149 5.0 A bromoacetyl strategy . 152 5.1. The strategy of the bromoacetyl system ; 152 5.2. Research targets in the form of glycosyhransferases 157 5.2.1. Ghitin synthase , - ^ _^ 157 5.2.2. Past and present antifungal agents: natural substrate mimics 159 5.3. The preparation of uridine 5'-0-monothiophosphate (UMPS) 162 5.4. The synthesis of activated bromoacetyl esters 166 5.5. The bromoacetyl Tripartite reaction: HOBt as the leaving group 168 5.6. Tripartite reaction over a range of pH: HOBt as the leaving group 171 5.7. Tripartate reaction: NHS as the leaving group 174 5.8. Ester hydrolysis and aminolysis 176 5.9. Studies of the pH-rate dependence of amine formation: Dipartite 'Click' chemistry 176 5.9.1.

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