Molecular dynamics simulations of sponge phase lipid nanoparticles
Abstract
Sponge phase lipid nano-particles (LNPs) for encapsulation of enzymes are of a high interest in a modern pharmaceutical industry. These therapeutics are very challenging for structural characterization due to their complexity, disorder and large sizes. For instance, each LNP can contain hundreds of thousands of large lipid molecules what can result in heavy and even non-converging calculations by crystallographic software using direct methods. Moreover, experimental data is ambiguous for such systems which requires to be explained by computer simulations on various levels: from atomistic to meso-scale. In this project multi-scale molecular dynamics (MD) simulations in combination with small-angle neutron scattering and neutron spin echo techniques will be used for structural refinement and investigation of pharmacological properties of therapeutic sponge phase LNPs. All-atom MD simulations will provide us more detailed structural information on smaller scale while simulations on coarse-grained level will reveal dynamics of large LNPs loaded with enzymes. Furthermore, newly derived models will become available for the whole computational community in order to help to develop more advanced medicines against cancer, Alzheimer's, Parkinson's and many other diseases. Gromacs software is seen as a powerful tool for performing the task on the latest high-performance computing systems at the National Supercomputer Center.
