TTeecchhnnoollooggiiccaall UUnniivveerrssiittyy DDuubblliinn AARRRROOWW@@TTUU DDuubblliinn Doctoral Science 2008-9 DDeessiiggnn aanndd SSyynntthheessiiss ooff CCaarrbboohhyyddrraattee BBaasseedd DDeerriivvaattiivveess aass AAnnttiimmiiccrroobbiiaall CCoommppoouunnddss Aoife Smith Technological University Dublin Follow this and additional works at: https://arrow.tudublin.ie/sciendoc Part of the Food Science Commons RReeccoommmmeennddeedd CCiittaattiioonn Smith, A. (2008). ,i>Design and Synthesis of Carbohydrate Based Derivatives as Antimicrobial Compounds. Doctoral Thesis. Technological University Dublin. doi:10.21427/D7H88N This Theses, Ph.D is brought to you for free and open access by the Science at ARROW@TU Dublin. It has been accepted for inclusion in Doctoral by an authorized administrator of ARROW@TU Dublin. For more information, please contact [email protected], [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 4.0 License Design and Synthesis of Carbohydrate Based Derivatives as Antimicrobial Compounds A THESIS SUBMITTED TO DUBLIN INSTITUTE OF TECHNOLOGY IN FULFILMENT OF THE REQUIREMENTS FOR THE AWARD OF DOCTOR OF PHILOSOPHY Aoife Smith B.Sc. School of Food Science and Environmental Health, Dublin Institute of Technology, Cathal Brugha St., Dublin 1. September 2008 Research Supervisors: Dr. Julie Dunne Dr. Paula Bourke Dr. Gary Henehan ABSTRACT Investigations into the design of analogues of GlcNAc-Ins, the substrate for the enzyme GlcNAc-Ins deacetylase (mshB), a therapeutic target on the pathway to mycothiol biosynthesis in Mycobacterium tuberculosis are described. Initial studies directed towards the design of a substrate analogue were based on the 3-D structure and a proposed mechanism of action of mshB (deduced by Dr. Andrew McCarthy, EMBL). The compounds were designed with the aim to produce an analogue which could better mimic the natural substrate for mshB (GlcNAc-Ins) for crystallisation and mechanistic studies to further improve the knowledge of this enzyme. A series of fatty acid ester and ether derivatives were designed and synthesised based on carbohydrate and non-carbohydrate polyhydroxylated scaffolds with a view to testing their antimicrobial activity against microorganisms of concern to the food and healthcare industries. The synthesised compounds, along with their corresponding fatty acid monoglyceride antimicrobials, were evaluated for antimicrobial activity against Staphylococcus aureus and Escherichia coli. Of the derivatives synthesised several of the carbohydrate based compounds have antimicrobial efficacy comparable with commercially available antimicrobials. The results suggest that the nature of the carbohydrate core plays a role in the efficacy of carbohydrate fatty acid derivatives as antimicrobials. DECLARATION I certify that this thesis which I now submit for examination for the award of Doctor of Philosophy, is entirely my own work and has not been taken from the work of others, save and to the extent that such work has been cited and acknowledged within the text of my work. This thesis was prepared according to the regulations for postgraduate study by research of the Dublin Institute of Technology and has not been submitted in whole or in part for an award in any other Institute or University. The work reported on in this thesis conforms to the principles and requirements of the Institute’s guidelines for ethics in research. The Institute has permission to keep, to lend or to copy this thesis in whole or in part, on condition that any such use of the material of the thesis be duly acknowledged. Signature Date ACKNOWLEDGEMENTS This research project would not have been possible without the support of many people. I wish to express my gratitude to my supervisor Dr Julie Dunne who was abundantly helpful and offered invaluable assistance, support and guidance. Deepest gratitude is also due to Dr Paula Bourke and Dr Gary Henehan, whose knowledge and assistance were invaluable to this study. In my daily work I have been blessed with a friendly and helpful group of fellow students. Special thanks go to Mark O’Connor and Andrew Kellett for all the fun in the lab. Mark I am indebted to you for listening to my endless chromatography woes and for your endeavours to keep the lab tidy. Not forgetting Aoife O’Gorman for her support, entertainment and of course for “Fab Fridays”. I would also like to convey thanks to Noel Grace, who was particularly obliging and offered invaluable assistance. He is a fine technician who kept me in Nitrogen and Acetone against all odds. I also wish to express my love and gratitude to my family for encouraging and supporting me throughout all of my studies. This dissertation is simply not possible without them. Special thanks go to Karl whom I am indebted to for his endless patience, understanding and support throughout this process. Lastly, I offer my regards to all of those who supported me in any respect during the completion of this project. SYMBOLS AND ABBREVIATIONS α alpha Å angstrom Ac acetate anhydr anhydrous apt t apparent triplet (spectral) aq. Aqueous β beta Bn benzyl br s broad singlet Bz benzoyl c concentration cm-1 wavenumber C=O carbonyl bond  chemical shift in ppm downfield from TMS C degrees Celsius d doublet (spectral) dd doublet of doublets (spectral) ddd doublet of doublets of doublets (spectral) equiv. equivalents Et ethyl FTIR fourier transform infrared g gram(s) h, min hour(s), minute(s) HATU N,N,N’,N’-tetramethyl-O-(7-azabenotriazol-1- yl)uronium hexaflurophosphate HAOt 1-hydroxy-7-aza-benzotriazole Hz hertz J coupling constant (nmr), in Hz L litre lit. literature reference LRMS-ES low resolution mass spectrometry-electrospray ionization m multiplet M molar M+ mass of the molecular ion (mass spectrometry) Me methyl mg milligram MHz megahertz mL milliliter mol, mmol mole, millimole M, mM micromolar, millimolar NMR nuclear magnetic resonance Ph phenyl PMB paramethoxybenzyl ppm parts per million (nmr) q quartet (spectral) R retention factor f rt room temperature [α] specific rotation D s singlet (spectral) t triplet (spectral) TIPS triisopropylsilyl t.l.c. thin layer chromatography Trityl triphenylmethyl SOLVENTS AND REAGENTS AcOH acetic acid Ac O acetic anhydride 2 AlCl aluminium chloride 3 BF ·Et O boron trifluoride·etherate 3 2 BnBr benzyl bromide BrCH OCH bromomethyl methylether 2 3 Bu NI tetrabutylammonium iodide 4 Bu SnO dibutyltin oxide 2 Bu Sn(MeO) dibutyltin dimethoxide 2 2 BzCl benzoyl chloride CAN cerric ammonium nitrate CDCl deuterio chloroform 3 CHCl chloroform 3 CH Cl dichloromethane 2 2 CSA camphorsulfonic acid CuSO .5H O copper sulfate pentahydrate 4 2 DAST diethylaminosulfur trifluoride DBU 1,8-diazabicyclo[5.4.0]undec-7-ene DDQ 2,3-dichloro-5,6-dicyano-1,4-benzoquinone DMAP 4-N,N dimethylaminopyridine DMF N,N dimethylformamide DMSO dimethylsulfoxide D O deuterium oxide 2 EtOAc ethyl acetate EtOH ethanol Et O diethylether 2 H hydrogen gas 2 HCl hydrochloric acid H O water 2 H SO sulfuric acid 2 4 Im. Imidazole IR 120 (H+) ion exchange resin (IR 120+) K CO potassium carbonate 2 3 LaCl lauroyl chloride LiAIH lithium aluminium hydride 4 MeCN/CH CN acetonitrile 3 MeOH methanol 4-MeOPhCH(OMe) 4-methoxy benzaldehyde dimethyl acetal 2 MgSO magnesium sulfate 4 MOMCl/CH OCH Cl chloromethyl methylether 3 2 NaCl sodium chloride NaCNBH sodium cyanoborohydride 3 NaH sodium hydride NaHCO sodium hydrogen carbonate 3 NaOH sodium hydroxide NaOMe sodium methoxide NAP 2-naphthylmethyl NH Cl ammonium chloride 4 NIS N-iodosuccinimide Pd-C palladium on charcoal PhCH(OMe) benzaldehyde dimethylacetal 2 PhH benzene PhSOTf phenylsulphenyl triflate PMBCl paramethoxybenzyl chloride PPL porcine pancreatic lipase Py pyridine TBAF tetrabutylammonium fluoride TBAI tetrabutylammonium iodide TEA triethylamine TFA trifluoroacetic acid THF tetrahydrofuran TIPSCl triisopropylsilyl chloride TMSOTf trimethylsilyl triflate TMSCl trimethylsilyl chloride TrCl triphenylmethyl chloride TsOH/pTSA p-toluenesulfonic acid