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Exploiting Aldolase Variants in the Synthesis of Fluorinated Analogues of N-Acetyl Neuraminic Acid

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Exploiting Aldolase Variants in the Synthesis of Fluorinated Analogues of N-Acetyl Neuraminic Acid Exploiting aldolase variants in the synthesis of fluorinated analogues of N-acetyl neuraminic acid Jennifer Ann Stockwell Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Astbury Centre for Structural Molecular Biology and Department of Chemistry September 2013 The candidate confirms that the work submitted is her own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. ©2013 The University of Leeds and Jennifer Ann Stockwell The right of Jennifer Ann Stockwell to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. i Acknowledgements I'd like to start off by thanking my supervisors Prof. Adam Nelson and Prof. Alan Berry for all the help and guidance they have given me over the last four years. Without their support, I wouldn't be sitting here writing these acknowledgements. I'd also like to thank my industrial supervisor Dr. Keith Mulholland, it was with his support and friendship that I was able to gain confidence and realise what I wanted to do with my life. My time at AstraZeneca was brilliant and there are too many people to thank individually, so I would like to say thank you all for making me feel so welcome. I would particularly like to thank Dr. Adam Daniels and Claire Windle for all their contributions, to Adam for his brilliant work towards greater understanding of the enzyme mechanism and to Claire for her beautiful crystal structure. I would also like to thank Dr. Tomas Lebl from the University of St. Andrews for all his help with the 2D 19F NMR studies. Thank you also to the support staff at the University of Leeds; Martin Huscroft for his help with HPLC, Simon Barrett for his help with NMR and Tanya Marinko-Covell for providing the HRMS service. I'd also like to thank all the past and present members of the Nelson and Berry groups for their support and contributions. Next I would like to thank my proof readers. Richard Doveston you have been brilliant, thank you so much for all your help. Also, thank you to my wonderful boyfriend Nathan Chapman; even though you had no idea what I was on about, you were still brilliant at picking out the times when I'd just written incomprehensible and grammatically incorrect gibberish. Also, thank you to Nathan for keeping me sane over the last few months. I'd like to thank my family. My parents, for motivating me and for staying calm when I was at my most stressed. Finally, I'd particularly like to thank my two grandfathers who unfortunately didn't live long enough to see me fulfil my dreams, but supported me throughout my education and would be so proud to see me now. ii Thank you Grandpa and Grandad Ken Harrington Ken Stockwell 1919 - 2007 1924 - 2013 iii Abstract This thesis reports the use of NAL variants to catalyse the reaction between a range of aldehyde analogues and fluoropyruvate, generating two new stereogenic centres. These reactions were catalysed by variants of N-acetyl neuraminic acid lyase (NAL). Wild-type NAL catalyses the aldol reaction between pyruvate and N-acetyl mannosamine (ManNAc) to give N-acetylneuraminic acid (Neu5Ac) whereas the NAL variants were evolved to catalyse the aldol reaction between pyruvate and the aldehyde analogue DHOB ([2R,3S]‐2,3‐dihydroxy‐4‐oxo‐N,N‐dipropylbutanamide) to give DPAH ([5R,6R]‐7‐(dipropylamino)‐4,5,6‐trihydroxy‐2,7‐dioxoheptanoic acid). This work has sought to explore the effect on the activity and stereoselectivity of the NAL variants with a broader range of substrates. A major challenge was the identification of the products of the NAL variant catalysed reactions and to determine the selectivity of each NAL variant. 19F NMR spectroscopy was invaluable in aiding characterisation of the enzyme reaction products. Synthesis of the enzyme substrate where X=NHAc has been of particular focus within this work and has provided further insight into the potential importance of the N- acetyl group in directing the binding of the aldehyde, therefore directing the diastereoselectivity. This work has also discovered that the introduction of fluorine may have an effect on the energy barrier to the transition state leading to the (4R) and (4S)-epimers of the products. However, in the case of more sterically demanding aldehydes, the diastereoselectivity is predominantly driven by the initial binding mode. This work has provided a more in-depth understanding of the effect of changing both the donor and acceptor substrates of the NAL-catalysed reaction. It has also evaluated the viability of using NAL variants in the synthesis of fluorinated analogues of N-acetyl neuraminic acid. iv Contents Acknowledgements .................................................................................................. ii Abstract ................................................................................................................... iv Contents ................................................................................................................... v List of Figures, Schemes, Tables and Charts ............................................................... x Abbreviations ....................................................................................................... xvii Chapter 1 Introduction ......................................................................................... 1 1.1 Relevance of fluorinated sialic acid analogues in medicinal chemistry .................. 2 1.1.1 Biological activity and applications of sialic acid analogues.................................... 2 1.1.2 The importance of fluorine in medicinal chemistry ................................................ 4 1.1.3 The gauche effect in organo-fluorine molecules .................................................... 5 1.1.4 Potential value of fluorinated sialic acid analogues ................................................ 6 1.2 Chemical methods for the synthesis of organo-fluorine molecules ....................... 7 1.2.1 Aldol reactions of -fluoro ketones ........................................................................ 7 1.2.2 Carbon-fluorine bond forming reactions ................................................................. 9 1.3 Wild type N-Acetyl-neuraminate lyase (NAL) ........................................................ 13 1.3.1 Mechanism of wild-type NAL................................................................................. 13 1.3.2 Substrate specificity of NAL ................................................................................... 18 1.4 Protein engineering of NAL E192N variants .......................................................... 22 1.4.1 Engineering of NAL variants with modified activity .............................................. 23 1.4.2 Identification of the NAL E192N variant and substrate specificity ....................... 24 1.4.3 Quantum mechanical/molecular mechanical studies of the active-site of NAL E192N .............................................................................................................................. 27 1.4.4 Discovery of a complementary pair of stereoselective enzymes .......................... 28 1.5 Thesis overview ..................................................................................................... 30 Chapter 2 Synthesis of Enzyme Substrates .......................................................... 32 v 2.1. Substrate Design .................................................................................................... 32 2.2. Synthesis of the stable alkene precursor of DHOB................................................ 34 2.3. Synthesis of a stable precursors of AHOB and ent-AHOB ..................................... 35 2.3.1. Retrosynthetic analysis of the stable precursors of AHOB/ent-AHOB .................. 35 2.3.2. Synthesis of AHOB utilising the Petasis reaction ................................................... 36 2.3.3. Reactions of the lactone intermediate 33 ............................................................. 42 2.3.4. Conversion of the lactone intermediate 35 into AHOB......................................... 46 Chapter 3 NAL-catalysed reactions of aldehyde analogues and pyruvate ............ 51 3.1 NAL E192N variants in the preparation of N-acetyl neuraminic acid analogues .. 51 3.1.1 Preparation of NAL variants and aldehyde substrates .......................................... 51 3.1.2 Preparative scale enzyme catalysed reactions of AHOB with pyruvate ................ 53 3.1.3 Identification and characterisation of AHOB enzyme catalysed reaction products .......................................................................................................................... 54 3.1.4 Measuring activity of the cleavage of the products of enzyme catalysed reactions .......................................................................................................................... 56 3.2 Monitoring enzyme catalysed reactions of AHOB by 500 MHz 1H NMR spectroscopy ................................................................................................................... 59 3.2.1 Comparison of activities and kinetic selectivity of enzyme catalysed reactions of AHOB ..............................................................................................................................
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