Scale-Down Characterisation of Post-Centrifuge Flocculation Processes and the Study of its Impact upon Downstream Processing during Mammalian Cell Antibody Production A thesis submitted to University College London for the degree of Doctor of Engineering by Georgina Espuny Garcia del Real December 2016 Department of Biochemical Engineering University College London Bernard Katz Building Gordon Street London WC1H 0AH Declaration Declaration I, Georgina Espuny Garcia del Real, confirm that the work presented in this thesis is my own. Where information had been derived from other sources, I confirm that this has been indicated in the thesis. Signature: Date: 09/12/2016 2 Abstract Abstract The high demand for biopharmaceuticals has been met thanks to improved upstream productivity. Downstream, which has not advanced at the same pace, calls for new clarification strategies to cope with the increased process-related impurities associated with upstream improvements. This thesis has focused on the implementation of polyelectrolyte flocculation between centrifugation and depth filtration during the primary recovery of a monoclonal antibody Chinese hamster ovary (CHO) cell process. A high-throughput, automated ultra scale-down (USD) flocculation methodology was developed with industrial relevance in mind for process development activities. The impact flocculation had on depth filtration and protein A chromatography performance was subsequently investigated and supported by analytical assays and techniques to assess impurity removal. Cell densities at time of harvest > 20x106 cells.mL-1 were critical for flocculation to occur on centrifuged CHO cell cultures. Flocculant addition time limited the flocculation scale-up success between two vessels with different geometrical ratios and working volumes (1.5 L and 800 µL). The influence of mixing time scales (macromixing, mesomixing and micromixing) on this variable defined the USD flocculation scale-up basis, which was: predominance of micromixing in the vessels (flocculant addition time scale-up) and constant power input per unit volume (impeller speed scale-up). The implementation of constant pressure, single-layer USD filtration methods with flocculated feeds was precluded due to the low filter capacity values obtained (< 35 L.m-2). In contrast, constant flux filtration with multi-layer depth filters at laboratory scale reached manufacturing-scale filter capacity values (> 490 L.m-2). Flocculation achieved larger depth filtration capacities and lower process-related impurities before protein A chromatography when compared to the current manufacturing processing option. Post-protein A chromatography, the clear eluate obtained with flocculation contrasted with the turbid eluate of the current processing option. Mass spectrometry data confirmed the turbid eluate was mainly constituted of negatively charged CHO cell protein precipitates. 3 Acknowledgements Acknowledgements There are many people to whom I would like to express my gratitude for helping me bring this thesis to fruition. I would like to thank my academic supervisor Dr Daniel Bracewell and my industrial supervisor Dr Jim Davies for their guidance, help and support that have undoubtedly contributed to keeping my work on track. I would also like to thank Dr Lee Allen and Dr Evi Dimitriadou, both from Lonza Biologics (Slough, UK), for their input and help during the early stages of this project, Dr Katherine Lintern for sharing her expertise in mass spectrometry analytical studies, and Prof Nigel Titchener-Hooker for the invaluable opportunity given. I would also like to thank the Engineering and Physical Sciences Research Council (EPSRC) and Technology Strategy Board (TSB) for funding this project. On a more personal note, I would like to thank my late grandmother for her unlimited patience and love, and for teaching me everything she knew from a very early age; my parents for their constant support, for always being by my side and for the sacrifices made, particularly during the past decade; Eduardo for always being the best version of himself, for his help and care, for the laughter and for the amazing travels together. Finally, I also want to thank my Catalan and Basque friends, particularly Alba, Anna and Hasier, with whom I have been able to share the ups and downs of our doctoral lives. 4 In the loving memory of my yaya, the strongest, most loving and hard-working woman I will ever encounter 5 Table of Contents Table of Contents Declaration ....................................................................................................................................2 Abstract ..........................................................................................................................................3 Acknowledgements .....................................................................................................................4 Table of Contents .........................................................................................................................6 List of Figures ............................................................................................................................. 14 List of Tables .............................................................................................................................. 18 Nomenclature ............................................................................................................................ 20 Abbreviations ............................................................................................................................ 27 1. Introduction .......................................................................................................................... 30 1.1. Antibodies for Therapeutic Use ........................................................................................................ 30 1.1.1. Monoclonal Antibody (mAb) Structure .................................................................................. 30 1.1.2. Therapeutic mAbs and Antibody-Related Molecules ...................................................... 32 1.1.2.1. Therapeutic mAbs ...................................................................................................................... 32 1.1.2.2. IgG-Based Bispecific Antibodies .......................................................................................... 32 1.1.2.3. Antibody Fragments (Fabs) ................................................................................................... 32 1.1.2.4. Domain Antibodies (dAbs) ..................................................................................................... 33 1.1.2.5. Fc-Fusion Proteins ..................................................................................................................... 33 1.1.2.6. Antibody-Drug Conjugates (ADCs)..................................................................................... 34 1.1.3. Market Analysis for Therapeutical mAbs .............................................................................. 34 1.2. Current Manufacturing Process for mAbs ................................................................................... 35 1.2.1. Cell Hosts ............................................................................................................................................... 36 1.2.2. Cell Culture ........................................................................................................................................... 37 1.2.3. Primary Recovery ............................................................................................................................. 37 1.2.4. Purification ........................................................................................................................................... 38 1.2.5. Ultrafiltration/Diafiltration (UF/DF) ...................................................................................... 39 1.3. Current Manufacturing Challenges in mAb Production and Proposed Solutions .... 40 1.3.1. Challenges ............................................................................................................................................. 40 1.3.1.1. Increasing Cell Densities ......................................................................................................... 40 1.3.1.2. Precipitation and Non-Specific Binding during Protein A Chromatography . 40 1.3.1.3. Ultra-High Protein Concentrations during UF/DF...................................................... 41 1.3.2. Potential Solutions during Primary Recovery..................................................................... 41 1.3.2.1. Expanded Bed Adsorption (EBA) Chromatography .................................................. 41 1.3.2.2. Aqueous Two-Phase Systems (ATPS) ............................................................................... 42 6 Table of Contents 1.3.2.3. Crystallisation............................................................................................................................... 43 1.3.2.4. Precipitation .................................................................................................................................. 43 1.3.2.5. Flocculation ................................................................................................................................... 44 1.3.3. The Fundamentals of Polyelectrolyte Flocculation .........................................................