Atomistic and coarse-grained modeling of polyethyleneimine

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

In silico prediction of the in vitro behavior of polymeric gene delivery vectors

Non-viral gene delivery vectors have increasingly come under the spotlight, but their performaces are still far from being satisfactory. Therefore, there is an urgent need for forecasting tools and screening methods to enable the development of ever more effective transfectants. Here, coarse-grained (CG) models of gold standard transfectant poly(ethylene imine)s (PEIs) have been profitably used to investigate and highlight the effect of experimentally-relevant parameters, namely molecular weight (2 vs. 10 kDa) and topologies (linear vs. branched), protonation state, and ammine-to-phosphate ratios (N/Ps), on the complexation and the gene silencing efficiency of siRNA molecules. The results from the in vitro screening of cationic polymers and conditions were used to validate the in silico platform that we developed, such that the hits which came out of the CG models were of high practical relevance. We show that our in silico platform enables to foresee the most suitable conditions for the complexation of relevant siRNA-polycation assemblies, thereby providing a reliable predictive tool to test bench transfectants in silico, and foster the design and development of gene delivery vectors.

Martini Force Field for Protonated Polyethyleneimine

Polyethyleneimine (PEI), one of the most widely used nonviral gene carriers, was investigated in the presented work at coarse-grained (CG) level. The main focus was on elaborating a realistic CG force field (FF) aimed to reproduce dynamic structural features of protonated PEI chains and, furthermore, to enable massive simulations of DNA-PEI complex formation and condensation. We parametrized CG Martini FF models for PEI in polarizable and nonpolarizable water by applying Boltzmann inversion techniques to all-atom (AA) probability distributions for distances, angles, and dihedrals of entire monomers. The fine-tuning of the FFs was achieved by fitting simulated CG gyration radii and end-to-end distances to their AA counterparts. The developed Martini FF models are shown to be well suited for realistic large-scale simulations of size/protonation-dependent behavior of solvated PEI chains, either individually or as part of DNA-PEI systems. © 2019 Wiley Periodicals, Inc.