Analysis and prediction of aggregation and degradation in protein-based biopharmaceuticals

Zidar, Mitja (author), Ravnik, Miha (mentor)

Research in protein aggregation and other degradation routes is of major importance in recent years, influencing the quality and consistency of biopharmaceutical drugs used to treat various life-threatening conditions. In this work we study the open soft-matter physics questions behind such processes that affect developability, safety and efficacy of aqueous solutions of therapeutic proteins. The focus lies on processes of irreversible aggregation and reversible self-association, which can be most influenced by the physical properties of the solution. Physico-chemical interactions reflected in colloidal and conformational stability are evaluated with dynamic light scattering (DLS) and induced protein denaturation. Thermal denaturation is measured via differential scanning calorimetry (DSC). Guanidium hydrochloride and urea are used as chemical denaturants and the ensuing unfolding is measured via tryptophan fluorescent response. The physical effect of excipients such as salts and sugars on protein stability is evaluated. Irreversible aggregation is accelerated mostly with elevated temperature and measured with size exclusion chromatography (SEC), resonant mass measurement (RMM) and micro-flow imaging (MFI). A Smoluchowski type system of differential equations, describing the kinetics of binary aggregation on multiple size scales, is numerically solved in parallel, with the model output compared with experimental data, explaining several phenomena specific to protein aggregation. Adhesion of proteins and protein particles in the micrometer size range to surfaces of containers is characterised with atomic force (AFM) and optical microscopy. We identify several different regimes of particle formation, adhesion to surfaces, and accumulation in bulk solution, shown to have a major impact on determination of particle formation propensity based on elevated temperature studies. We evaluate the discrepancies with mean-field Smoluchowski type models in this non-colloidal regime. Reversible self-association resulting in increased solution viscosity is measured with microfluidic rheometry. The factors contributing to viscosity of protein solutions are analysed and evaluated. A novel interaction mechanism contributing to viscosity is proposed. Finally, this work is a contribution towards advanced protein formulation development with special emphasis on development of biopharmaceuticals.

• Language: English
• Keywords: soft matter physics, monoclonal antibody, aggregation, degradation, viscosity, biopharmaceuticals, proteins
• Work type: Doctoral dissertation
• Typology: 2.08 - Doctoral Dissertation
• Organization: FMF - Faculty of Mathematics and Physics
• Year: 2020
• PID: 20.500.12556/RUL-117659
• COBISS.SI-ID: 23998723
• Publication date in RUL: 19.07.2020

ZIDAR, Mitja, 2020, Analysis and prediction of aggregation and degradation in protein-based biopharmaceuticals [online]. Doctoral dissertation. [Accessed 26 April 2025]. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=117659

Secondary language

• Language: Slovenian
• Title: Analiza in napoved združevanja ter razgradnje proteinov v bioloških zdravilih

Abstract

V zadnjih letih narašča pomembnost raziskav procesov kot so agregacija in degradacija proteinov, ki vplivajo na kvaliteto bioloških zdravil za zdravljenje različnih bolezenskih stanj. V tezi raziskujemo tematike fizike mehke snovi v povezavi s temi procesi, od katerih zavisi razvoj, varnost in učinkovitost vodnih raztopin terapevtskih proteinov. Osredotočamo se predvsem na procese nereverzibilne agregacje in reverzibilnega povezovanja proteinskih molekul, na katere lahko v veliki meri vplivamo s fizikalnimi lastnostmi raztopin. Fizikalno-kemijske interakcije, ki vplivajo na koloidno in konformacijsko stabilnost, ovrednotimo z dinamičnim sipanjem svetlobe (DLS) in denaturacijo. Termično denaturacijo merimo z diferencialno kalorimetrijo (DSC). Kot denaturante za kemično denaturacijo uporabljamo gvanidinijev klorid in ureo, merimo pa jo prek fluorestenčnega odziva triptofanov. Ovrednotimo fizikalni vpliv pomožnih snovi v zdravilu (ekscipientov), kot so soli in sladkorji. Tvorbo nereverzibilnih agregatov pospešimo s povišano temperaturo in merimo z izključitveno kromatografijo (SEC), resonančnim merjenjem mase (RMM) in pretočno mikroskopijo (MFI). Vzporedno z eksperimentom numerično rešimo sistem enačb po vzoru Smoluchowskega, ki opisujejo kinetiko binarne agregacije na večih velikostnih skalah, in primerjamo dobljene rezultate z eksperimentom. Tako pojasnimo osnovne pojave, povezane z agregacijo proteinov. Z mikroskopom na atomsko silo (AFM) in optično mikroskopijo raziskujemo adhezijo proteinov in proteinskih delcev na površine vsebnikov. Opišemo več režimov tvorbe delcev v raztopini in njihovega prijemanja na površine, ki imajo pomemben vpliv na interpretacijo rezultatov meritev vsebnosti delcev po študijah pri povišani temperaturi. Komentiramo tudi odstopanje rezultatov od teoretičnih napovedi modela Smoluchowskega zaradi posedanja in adhezije. Reverzibilno povezovanje proteinskih molekul, katerega makroskopski vpliv se kaže v povišani viskoznosti, merimo z mikrofluidno reometrijo. Razločimo in analiziramo različne faktorje, ki vplivajo na viskoznost. Predlagamo nov mehanizem, ki povezuje povišanje viskoznosti z elektrostatskimi interakcijami. To delo prispeva k napredku razvoja proteinskih formulacij, s posebnim poudarkom na razvoju bioloških zdravil.

• Keywords: fizika mehke snovi, monoklonsko protitelo, agregacija, degradacija, viskoznost, biološka zdravila, proteini