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Antibody Conjugates: Integrated Approach Towards Selective, Stable and Controllable Bioconjugation

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Antibody Conjugates: Integrated Approach Towards Selective, Stable and Controllable Bioconjugation Antibody conjugates : integrated approach towards selective, stable and controllable bioconjugation Igor Dovgan To cite this version: Igor Dovgan. Antibody conjugates : integrated approach towards selective, stable and controllable bioconjugation. Organic chemistry. Université de Strasbourg, 2017. English. NNT : 2017STRAF036. tel-02872896 HAL Id: tel-02872896 https://tel.archives-ouvertes.fr/tel-02872896 Submitted on 18 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES CHIMIQUES UMR 7199, Laboratoire des Systèmes Chimiques Fonctionnels THÈSE présentée par : Igor DOVGAN soutenue le : 21 septembre 2017 pour obtenir le grade de : Docteur de l’Université de Strasbourg Discipline/ Spécialité : Chimie Organique Antibody conjugates: integrated approach towards selective, stable and controllable bioconjugation THÈSE dirigée par : WAGNER Alain Docteur, Université de Strasbourg RAPPORTEURS : BIOT Christophe Professeur, Université de Lille 1 CHUDASAMA Vijay Docteur, University College London AUTRES MEMBRES DU JURY : CIANFÉRANI Sarah Docteur, Université de Strasbourg Leonardo da Vinci: “Where Nature finishes producing its own species man begins, with the help of Nature, to create an infinity of species” ACKNOWLEDGMENTS This PhD work has been carried out in the Laboratory of Functional Chemo-Systems (LFCS; currently BioFunctional Chemistry, BFC) of the Faculty of Pharmacy at the University of Strasbourg under the supervision of Dr. Alain Wagner and has received financial support from University of Strasbourg and Region Alsace. This work could not be possible also without acknowledging a number of people who supervised me, helped me and supported me over the past three years. First of all, I would like to thank my PhD supervisor Dr. Alain Wagner for giving me an opportunity to work on the fascinating projects and for the freedom and confidence I was gained to realize them. I wish to acknowledge all his support and encouragement during my research and his constant enthusiasm towards my sometime naïve ideas. I would also like to express my thanks to jury members: Prof. Christophe Biot from the University of Lille and Dr. Vijay Chudasama from the University College London for examining my work, Dr. Sarah Cianférani from the University of Strasbourg for the acceptance to be the President of this committee and Dr. Sergii Kolodych from Syndivia for his willingness to participate in the thesis discussion. I am very grateful to those who helped me on my early stage in the lab: Oleksandr Koniev for the course of organic synthesis and experiment settings, for his invariable and relentless guidance to work hard; Sergii Kolodych for the wise supervision in bioconjugate chemistry and for our fruitful tea-time discussion about science and life. I would like to express my gratitude to those who helped my research to be done; Sylvain Ursuegui for the generous sharing of his linkers, the synthesis of oligonucleotide derivative and for the constant readiness to help. The LSMBO group – Stephane Erb, Anthony Ehkirch, Steve Hessmann, Sarah Cianferani, and Alain van Dorsselaer – for the realisation of the screening project. Our new permanent, Guilhem Chaubet, for his help with the thesis proofread. All the colleges from our UMR; in particular Eric and Celia for the time spend together and our funny journey to Amsterdam, Manon for the successful projects done together. Enormous thank you to all my friends from Strasbourg, who were always near to help or to have fun: Nina, Anna D, Anna Z, Natalia, Viktoriia, Diana, Olga, Kon’ko, Iiulia D. & Dima D., Simon, Vuk, Joe. To Kyong for making me his very tasty cappuccino during my thesis writing. To my friends from Toulouse: Roberto, Marie and Emmanuelito, thanks a lot guys for your friendship and our crazy parties! To my friends from Ukraine: Vetalka, Kolya, Magir, Danil, Viktor, Levko, Oleg for being in contact, even after so many years being in distance. A special thanks to Artem Osypenko who has motivated me to come in France and for our perpetual philosophic evening spent together that I liked so much. To Dima Kandaskalov for his tutoring in chemistry during my preparation to chemical Olympiads (the best teacher ever). I thank my wife for her love, her constant support and believe in me, for her patience and her courage. I would like to thank all my family, especially my mum and sister for their love and support throughout my life. ABBREVIATIONS ABF p-Azidobenzoyl Fluoride ABNHS p-Azidobenzoyl N-Hydroxysuccinimide ACs Antibody Conjugates ADCs Antibody-Drug Conjugates ADCC Antibody-Dependent Cell-Mediated Cytotoxicity AOCs Antibody-Oligonucleotide Conjugates APG p-Azidophenyl Glyoxal Monohydrate APN 3-Arylpropiolonitriles BBS Borate Buffered Saline BCN Bicyclo[6.1.0]Nonyne BHQ Black Hole Quencher BME Β-Mercaptoethanol CBTF 4-((4-(Cyanoethynyl)Benzoyl)Oxy)-2,3,5,6-Tetrafluorobenzenesulfonate CuAAC Copper(I)-Catalysed Alkyne-Azide Cycloaddition DCC N,N’-Dicyclohexylcarbodiimide DCM Dichloromethane DIBO Dibenzoazacyclooctyne DIPEA N,N-Diisopropylethylamine DMF Dimethylformamide DoC Average Degree Of Conjugation DTT Dithiothreitol EDC, EDCI 1-Ethyl-3-(3-Dimethylaminopropyl)Carbodiimide EDTA Ethylenediaminetetraacetic Acid Fab Fragment Antigen-Binding FBDP Formylbenzene Diazonium Hexafluorophosphate FcRn Neonatal Fc Receptor FDA U.S. Food And Drug Administration HATU 1-[Bis(Dimethylamino)Methylene]-1H-1,2,3-Triazolo[4,5-B]Pyridinium3- Oxide Hexafluorophosphate HBTU O-Benzotriazole-N,N,N’,N’-Tetramethyl-Uronium Hexafluorophosphate HIV Human Immunodeficiency Virus HOBt Hydroxybenzotriazole HRMS High Resolution Mass Spectrometry IC50 Half Maximal Inhibitory Concentration LCMS Liquid Chromatography Mass Spectrometry LRMS Low Resolution Mass Spectrometry i mAb Monoclonal Antibody MAPN p-(Maleimide)-Phenylpropiolonitrile Sodium 4-(Maleimidomethyl)-1,3-Dioxane-5-Carbonyl)Oxy)-2,3,5,6- MDTF Tetrafluorobenzenesulfonate MS Mass Spectroscopy MWCO Molecular Weight Cut Off native-HRMS High Resolution Native Mass Spectrometry NHS N-Hydroxysuccinimidyl NMR Nuclear Magnetic Resonance PCR Polymerase Chain Reaction PB Phosphate Buffer PBS Phosphate Buffered Saline PEG Polyethylene Glycol PTAD 4-Phenyl-3h-1,2,4-Triazole-3,5(4h)-Dione PyBOP (Benzotriazol-1-Yloxy)Tripyrrolidinophosphonium Hexafluorophosphate RNA Ribonucleic Acid SDS-PAGE Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis SMCC N-Succinimidyl-4-(Maleimidomethyl)-Cyclohexanecarboxylate SPAAC Strain-Promoted Alkyne–Azide Cycloadditions STP Sodium 2,3,5,6-Tetrafluoro-4-Hydroxybenzene-1-Sulfonate TAMRA Tetramethylrhodamine TCEP Tris(2-Carboxyethyl)Phosphine Hydrochloride TFA Trifluoroacetic Acid THF Tetrahydrofuran TLC Thin Layer Chromatography Tris Tris(Hydroxymethyl)Aminomethane UV-Vis Ultraviolet-Visible Spectrophotometry ii TABLE OF CONTENTS A. Introduction ................................................................................................................................ 1 1 Bioconjugate chemistry ........................................................................................................... 1 2 Antibody conjugates ................................................................................................................ 1 2.1 Antibodies ........................................................................................................................ 2 2.2 Antibody structure ............................................................................................................ 3 2.3 Antibody-drug conjugates ................................................................................................ 5 3 Chemical approach for antibody conjugation .......................................................................... 7 3.1 Bioorthogonal reaction and click chemistry .................................................................... 7 3.2 Strategies for antibody functionalisation ......................................................................... 8 3.3 Aspartic and glutamic acid ............................................................................................... 9 3.4 Lysine residues ............................................................................................................... 10 3.5 Cysteine residues ............................................................................................................ 14 3.6 Disulfide rebridging ....................................................................................................... 19 3.7 Tyrosine residues ........................................................................................................... 23 3.8 Arginine residues ........................................................................................................... 27 3.9 Tryptophan residues ....................................................................................................... 28 3.10 Methionine residues ....................................................................................................
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