Assessment of Protein Aggregation in Biotherapeutic Development and Biomarker Detection

Abstract

Proteins are complex macromolecules which have been developed by Nature to perform defined biological functions. Their sequences confer them unique biochemical and biophysical properties and allows proteins to interact with desired targets or self-assemble into functional assemblies. These complex interactions can however also lead to the formation of aberrant protein aggregates. Aggregation is challenging to describe and predict because of the extensively broad time and length scales associated with the process, the heterogeneity of the species involved, for instance in terms of size and reactivity, and the complex environment in which proteins typically evolve. Today, there is therefore still a strong need for in silico tools and analytical methods that can provide informative data on protein biophysical properties and aggregation in a high-throughput manner and with higher quality. In this context, the present thesis aims at developing new biophysical tools compatible with high-throughput development to inform on protein state in solution and help rationalizing protein aggregation, with applications in biologics development and for biomarker detection. The first part of the thesis proposes microfluidic and nanotechnology-based tools for the development of safe biopharmaceuticals. We present a microfluidic diffusion sizing platform which is able to size protein aggregates in the submicron range, and probe for viscosity and interactions directly in highly concentrated protein solutions, which represent key quality attributes of the biopharmaceutical product. Then, we describe a nanoparticle-based assay to quantitatively assess the effect of surfaces on protein stability, which has been identified as one of the major causes of aggregation but is still very poorly characterized.We demonstrate applications of this platform for “developability” studies to screen for optimal protein or formulation candidates. The second part of the thesis focuses on the detection of biomarkers. We describe a generic approach to detect biomarkers with undefined biochemical and biophysical properties, for instance protein aggregates or extracellular vesicles. The platform is based on a microfluidic shrinking droplet concentrator device that locally upconcentrates the analyte to enable its detection. The device can also be applied to generate protein phase diagrams and mimic a type of cellular compartmentalization under stress. Finally, we present a new bioseparation platform which is able to isolate ppm amounts of target compounds directly from complex mixtures. The tool is based on synthetic microdroplets that are designed to preferentially exclude a wide range of compounds, and functionalized with a binding moiety which allows to specifically recruit and locally upconcentrate desired biomarkers. Overall, we propose a range of new analytical platforms which can complement the pool of existing biophysical characterization tools and inform in a quantitative manner on protein aggregation events in solution. These new analytical methods can contribute to a more efficient development of biopharmaceuticals by filling the current severe need for high-throughput, quantitative and informative experimental techniques. The collected experimental information may be used as input for advanced computational tools which could use this higher quality data to better describe protein behavior in solution and predict potential liabilities, ultimately guiding protein candidate selection and rationalizing the impact of formulation conditions. In the context of pathological protein aggregation in vivo, the platforms provide initial steps to isolate key players involved in the aggregation process, with potential implications in both the fundamental understanding of the aggregation process and the improvement of diagnostic biomarker detection.