Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison.

Kabedev A, Bergström CAS, Larsson P

J Comput Aided Mol Des 38 (1) 5 [2023-12-16; online 2023-12-16]

Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important for the development of new delivery techniques and bioavailability improvement. A balance between accuracy and computational cost is a key factor for an extensive study of numerous compounds in diverse environments. In this study, we aimed to determine an optimal molecular dynamics (MD) protocol to evaluate small-molecule interactions with micelles composed of bile salts and phospholipids. MD simulations were used to produce free energy profiles for three drug molecules (danazol, probucol, and prednisolone) and one surfactant molecule (sodium caprate) as a function of the distance from the colloid center of mass. To address the challenges associated with such tasks, we compared different simulation setups, including freely assembled colloids versus pre-organized spherical micelles, full free energy profiles versus only a few points of interest, and a coarse-grained model versus an all-atom model. Our findings demonstrate that combining these techniques is advantageous for achieving optimal performance and accuracy when evaluating the solubilization capacity of micelles. All-atom (AA) and coarse-grained (CG) umbrella sampling (US) simulations and point-wise free energy (FE) calculations were compared to their efficiency to computationally analyze the solubilization of active pharmaceutical ingredients in intestinal fluid colloids.

Bioinformatics Support for Computational Resources [Service]

PubMed 38103089

DOI 10.1007/s10822-023-00541-1

Crossref 10.1007/s10822-023-00541-1

pmc: PMC10725378
pii: 10.1007/s10822-023-00541-1