THÈSE DE DOCTORAT DE L’UNIVERSITÉ D’AIX-MARSEILLE Soutenue par Phuong Chi NGUYEN Pour obtenir le grade de Docteur de l’Université d’Aix-Marseille Discipline: Biologie Spécialité: Microbiologie Deciphering antimycobacterial activity of Cyclophostin/Cyclipostins analogs and Oxadiazolones derivatives, two new promising family compounds in the treatment of tuberculosis and mycobacterial-related diseases Soutenue le 25 Mai 2018 devant le jury : Dr. Alain BAULARD (INSERM, Lille) Rapporteur Dr. Jean Denis PEDELACQ (IPBS, Toulouse) Rapporteur Dr. Véronique FONTAINE (ULB, Belgium) Examinatrice Pr. Sophie BLEVES (LISM, Marseille) Examinatrice-Présidente Dr. Céline CRAUSTE (IBMM, Montpellier) Examinatrice Dr. Stéphane CANAAN (LISM, Marseille) Directeur de thèse Acknowledgements I would like to take this opportunity to sincerely thank all people who have supported me during the time of my PhD. First and foremost, I offer the sincerest gratitude to my supervisor, Dr. Stéphane CANAAN. Thank you for your continuous support and guidance during the time I have spent in the group. I really appreciate your encouragement and excellent ideas whenever I was stuck. It has been 3 years since you offered me to come here. We have overcome many difficulties and now I am going to defense a good thesis. Thank you! Besides my supervisor, I would like to thank the rest of my thesis committee: Dr. Alain BAULARD and Dr. Jean Denis PEDELACQ, who have accepted to be reporters of this manuscript, Pr. Sophie BLEVÉS who has accepted as the president of the jury, Dr. Véronique FONTAINE and Dr. Céline CRAUSTE, for their acceptance as examiners. My sincere thanks goes to Dr. Jean-François CAVALIER, for advising me on the aspects of my work especially on biochemistry and chemistry. Thank you for your unwavering support during my time in the laboratory as well as be patient to correct all my manuscripts. I would take this opportunity to express my sincere gratitude to my wonderful colleagues. Thank you, Isabelle and Vanessa, for being kind and ready for help any time I need, despite of difference in language. Thanks Pierre for all your support through the time of my PhD with a lot of mini details have been discussed and solved to bring good results. Thanks Djalil for working together and produced two papers. I would also thank to two postdocs, Nabil and Ticiana, who shared their own knowledge, experiences and ideas. I also cannot thank enough to all Vietnamese students in Luminy and Marseille who make me feel at home even we live thousand miles away from our country. Thanks to brother Quan and sister Thuy for being so kind. I would also thank to French and foreigner students, I have had a great fortune of spending time with all of you. This acknowledgement would not be completed without mentioning endless love, support and encouragement from my husband and my family. Thank you for being always beside me and sharing all the joy and sorrow together. I am eternally thankful to my parents, my husband’s parents and my older brother. Thank you for your continuous encouragement. I am happy to have all beloved like you. Table of contents INTRODUCTION .................................................................................................................. 1 CHAPTER 1: General introduction ..................................................................................... 2 1.1. Tuberculosis, an overview ............................................................................................... 2 1.2. History timeline of Tuberculosis .................................................................................... 3 1.3. Diagnosis and vaccination ............................................................................................... 4 Diagnosis ................................................................................................................................... 4 Vaccines..................................................................................................................................... 5 1.4. Biological characteristics of M. tb .................................................................................. 6 General biology ......................................................................................................................... 6 Genome of M. tb ........................................................................................................................ 8 Cell envelope ............................................................................................................................. 9 1.5. Pathogenic life cycle ...................................................................................................... 12 Transmission ........................................................................................................................... 12 Initial infection ....................................................................................................................... 14 M. tb intracellular life ............................................................................................................. 14 Immune response to M. tb infection ........................................................................................ 14 Granulomas ............................................................................................................................. 15 1.6. Treatment of TB ............................................................................................................ 17 Standard treatment for TB ....................................................................................................... 17 Front-line drugs ...................................................................................................................... 17 1.7. Drug resistance and mechanisms .................................................................................. 21 1.8. Treatment in drug-resistance TB and new drugs development ................................. 23 Current treatment in drug-resistance TB ............................................................................... 24 New drugs in development ...................................................................................................... 25 1.9. Lipid metabolism of M. tb ............................................................................................. 26 CHAPTER II: Lipolytic enzymes in M. tb – the fundamental of a new drug family development .......................................................................................................................... 28 2.1. Serine hydrolase enzymes from M. tb: promising therapeutic targets ..................... 28 2.2. Mycobacterial lipolytic enzymes .................................................................................. 31 True lipases ............................................................................................................................. 32 Carboxylesterases ................................................................................................................... 35 Cutinases ................................................................................................................................ 37 Phospholipases ........................................................................................................................ 38 CHAPTER III: Inhibitors of lipolytic enzymes ................................................................. 40 3.1. Orlistat ............................................................................................................................ 40 3.2. Orlistat-core compounds .............................................................................................. 41 3.3. β-lactone EZ120 ............................................................................................................. 42 3.4. Lalistat ............................................................................................................................ 43 3.5. Oxadiazolone-core compounds .................................................................................... 45 3.6. Cyclophostin and Cyclipostins molecules .................................................................... 47 3.7. Activity-based protein profiling (ABPP), powerful chemical proteomic platform applied to investigate targets of CyC analogs and Oxadiazolones derivatives ............... 52 3.8. Objectives of my thesis .................................................................................................. 54 RESULTS .............................................................................................................................. 55 Article 1: Cyclipostins and Cyclophostin analogs as promising compounds in the fight against tuberculosis .............................................................................................................. 56 Article 2: Cyclophostin and Cyclipostins analogs, new promising molecules to treat mycobacterial-related diseases ............................................................................................ 84 Article 3: Cyclipostins and Cyclophostin analogs inhibit the antigen 85C from Mycobacterium tuberculosis both in vitro and in vivo ........................................................ 93 Article 4: A biochemical and structural characterization of TesA a major thioesterase requires for PDIM and PGL syntheses in M. tuberculosis ............................................. 110 Article