Towards an understanding of biomolecule partition in amphiphilic systems: development of a molecular dynamics framework

• Autor(a) principal: Bastos, Henrique Xavier Santos
• Data de Publicação: 2019
• Tipo de documento: Dissertação
• Idioma: eng
• Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
• Texto Completo: http://hdl.handle.net/10773/30274
• topic: Amphiphilic molecules; Ionic liquids; Molecular dynamics; All-atom; Coarse-grained; Biomolecules; Gallic acid; Ibuprofen; Drug delivery

Amphiphilic molecules are interesting building blocks of self-assembled structures for a variety of biotechnological purposes, due to their hydrophobic and hydrophilic moieties. Some of them are deemed as biocompatible, capable of carrying biomolecules, while being highly tuneable and controlled with external cues. Such properties are advantageous in drug delivery applications. Ionic liquids have gained relevance since their discovery as not only responsive and adjustable, but also as promising alternatives to conventionally used solvents. This project aims to use molecular dynamics to the study of ammonium-based ionic liquids in the extraction and delivery of biomolecules, specifically gallic acid and ibuprofen. A multiscale strategy was followed to simulate systems using the GROMACS package for classical molecular dynamics simulations. High-resolution descriptions were used to create a novel coarse-grained model to reproduce the phase behaviour and partition studies. The partition of gallic acid and ibuprofen in the studied ionic liquid solutions was assessed, as well as the particular orientation of the biomolecule in the supramolecular structure of the ionic liquids, as well as the interactions generating each outcome. A pH-driven effect was verified as the main parameter affecting the studied systems. This work has the potential to pave the way for a transferable, transversal platform to analyse and test different biomolecule-IL combinations in aqueous solutions in order to save time and experimental resources in diverse applications.