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Biomolecules As Recognition Elements for Bioactive Polyphenols in Coffee

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Biomolecules As Recognition Elements for Bioactive Polyphenols in Coffee UNIVERSITÀ DEGLI STUDI DI TRIESTE XXVI CICLO DEL DOTTORATO DI RICERCA IN SCIENZA, TECNOLOGIA ED ECONOMIA NELL’INDUSTRIA DEL CAFFÈ BIOMOLECULES AS RECOGNITION ELEMENTS FOR BIOACTIVE POLYPHENOLS IN COFFEE CHIM/06 Ph.D. Student Valentina Sinisi Ph.D. program Coordinator and Thesis Supervisor Dr. Federico Berti Thesis Co-supervisor Dr. Cristina Forzato ANNO ACCADEMICO 2012/2013 Odi et amo. Quare id faciam, fortasse requiris. Nescio, sed fieri sentio et excrucior.* Catullus, carmen 85 * I hate and I love. Wherefore would I do this, perhaps you ask? I do not know. But I feel that it happens and I am tormented. Table of contents Table of contents Table of contents .............................................................................................................................. i Abstract .............................................................................................................................................. v List of abbreviations ..................................................................................................................... xii Chapter 1 - Introduction ................................................................................................................. 1 1.1 Coffee polyphenols ................................................................................................................... 3 1.1.1 Coffee: a successful beverage ............................................................................................. 3 1.1.2 The composition of coffee .................................................................................................. 3 1.1.3 The aroma of coffee ............................................................................................................. 5 1.1.4 The taste of coffee ................................................................................................................ 5 1.1.5 Phenolic compounds ........................................................................................................... 6 1.1.5.1 Chlorogenic acids (CGAs) ............................................................................................... 7 1.1.5.2 Thermal transformation of CGAs ................................................................................... 9 1.1.5.3 Chlorogenic lactones (CGLs) ......................................................................................... 10 1.1.5.4 Chlorogenic compounds are absorbed in humans ......................................................... 12 1.2 Recognition and sensing elements ....................................................................................... 19 1.2.1 Sensors: biomolecules and their mimics ........................................................................ 19 1.2.2 Molecular recognition elements ...................................................................................... 20 1.2.2.1 Antibodies ...................................................................................................................... 20 1.2.2.2 Receptors ....................................................................................................................... 21 1.2.2.3 Lectins ........................................................................................................................... 21 1.2.2.4 Short peptides ............................................................................................................... 21 1.2.2.5 Aptamers ....................................................................................................................... 24 1.2.2.6 Peptide Nucleic Acids ................................................................................................... 25 1.3 Human Serum Albumin ......................................................................................................... 31 1.3.1 Human Serum Albumin as a starting point .................................................................. 31 1.3.2 HSA structure and properties .......................................................................................... 31 1.3.3 Binding sites ....................................................................................................................... 32 1.3.3.1 Site I .............................................................................................................................. 34 i Table of contents 1.3.3.2 Site II ............................................................................................................................. 36 1.3.4 Influence of endogenous ligands on HSA binding properties .................................... 37 1.4 HSA100 and mutant libraries ................................................................................................ 41 1.4.1 Directed evolution strategy .............................................................................................. 41 1.4.2 HSA100 ............................................................................................................................... 41 1.4.2.1 HSA100 identification and optimization ...................................................................... 41 1.4.2.2 Expression of HSA100 .................................................................................................. 42 1.4.3 HSA100 mutant libraries .................................................................................................. 44 1.4.3.1 Structural analysis ........................................................................................................ 44 1.4.3.2 HSA100 site-directed mutagenesis ............................................................................... 45 Chapter 2 - Aim of research ......................................................................................................... 47 2. Aim of research .......................................................................................................................... 49 Chapter 3 - Results and discussion ........................................................................................... 51 3.1 Quinides synthesis .................................................................................................................. 53 3.1.1 Synthesis of 3,4-O-dicaffeoyl-1,5--quinide (7) .............................................................. 53 3.1.2 Synthesis of 1,3,4-O-tris[3,4-(dimethoxy)cinnamoyl]-1,5--quinide (10), 3,4-O- bis[3,4-(dimethoxy)cinnamoyl]-1,5--quinide (11), and 3-O-[3,4-(dimethoxy)cinnamoyl]- 1,5--quinide (12) ........................................................................................................................ 55 3.1.3 Synthesis of 3-O-[4-(aminobutanamidoethoxy)feruloyl]-4-O-[3,4- (dimethoxy)cinnamoyl]-1,5--quinide (28) ............................................................................. 59 3.2 HSA, HSA100 and its mutants: interaction studies .......................................................... 65 3.2.1 Human serum albumin (HSA) ........................................................................................ 65 3.2.1.1 The choice of fluorescence spectroscopy ......................................................................... 65 3.2.1.2 Titration assays ............................................................................................................. 66 3.2.1.3 HSA fluorescence quenching ......................................................................................... 67 3.2.1.4 Stern-Volmer analysis ................................................................................................... 69 3.2.1.5 Dissociation constants and binding sites ...................................................................... 71 3.2.2 HSA100 and its mutants ................................................................................................... 77 3.2.2.1 Binding biomolecules and titration assays .................................................................... 77 3.2.2.2 Fluorescence quenching and dissociation constants ..................................................... 79 3.3 Surface Plasmon Resonance and Biacore assay ................................................................. 83 3.3.1 Surface Plasmon Resonance ............................................................................................. 83 3.3.2 Evaluation of the association constant ........................................................................... 85 3.3.3 The experiment .................................................................................................................. 86 ii Table of contents 3.4 NMR investigation on the caffeine-quinides interaction ................................................ 91 3.4.1 Caffeine interacts with polyphenols ............................................................................... 91 3.4.2 Study of the interaction between caffeine and the synthesized quinides ................. 91 3.4.2.1 Titrations of 7, 10, 11 and 12 with caffeine in DMSO-d6/D2O 75-25% ...................... 92 3.4.2.2 Titrations of 7 with caffeine in D2O/DMSO-d6 75-25% .............................................. 96 3.5 Antiviral assays ...................................................................................................................... 103 3.5.1 Further investigations of the bioactivity of the chlorogenic compounds ................ 103 3.5.2 Influenza virus ................................................................................................................
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