Multiscale Modeling of Chromatographic Systems: Insights into Protein Selectivity, Ligand Design and Methods Development

The development of efficient bioseparation processes for the production of high-purity biopharmaceuticals is one of the most pressing challenges facing the pharmaceutical and biotechnology industries today. Recent advances in the design of multi-modal chromatographic systems has produced new classes of chromatographic materials which can provide alternative and improved selectivities as compared to traditional single mode chromatographic materials. We have used a strategic approach to the development of simulations and experiments to examine the relevant interactions in these systems. This thesis focuses on the simulation efforts being used to probe binding and adsorption in these systems. By understanding both protein-ligand and protein-resin interactions through a range of molecular dynamics and coarse grained approaches the fundamental nature of selectivity can be illuminated. Coarse grained protein-surface docking simulations were performed to determine the preferred binding orientations for a range of proteins on ion-exchange surfaces. These results were related to work done using electrostatic potential isosurfaces to examine the chromatographic adsorption of homologous protein libraries. Molecular dynamics protein-ligand simulations were performed in free-solution to determine multimodal ligand binding sites on the protein surface. Importantly, these simulations were found to corroborate experimental data obtained with both NMR and chromatography experiments for a library of homologous protein mutants. Further, these MD simulations were conducted with a combinatorial ligand library to study the role of synergy in the determination of ligand binding sites for these "pseudo-affinity" ligands. Finally, all-atom MD simulations were performed to examine the binding of several proteins to self-assembled monolayers presenting relevant multi-modal ligands. This body of work has laid the foundation for a molecular level understanding of selectivity in multimodal chromatographic systems. Additionally, understanding the role of synergy in the determination of binding sites for multimodal ligands will play an important role in the further development of next generation ligands for important separation challenges.