Martini parameter files for stabilising excipient simulation

Abstract

Parameter files (.gro, .mdp) for the simulation of stabilising excipients, which were used to study protein-excipient interaction and gain insight into their structure-activity relationship. Protein formulations have issues surrounding their stability; currently, excipients are added to improve their colloidal and conformational stability. These are selected not for their ability to prevent aggregation per se but because of their exemplary safety profile. These excipients (polysorbates, Brij, fatty acid ethoxylates, fatty acids, sugars, liposaccharides, amino acids, phospholipids, glycerides, ceramides) were parameterised in the Martini forcefield or collected from the Martini website in order to be simulated in Gromacs and investigate the interaction between excipients and protein at high resolution, and probe the mechanism of aggregation-prone region shielding. These were used in the study of two proteins: HSA and insulin.