(M1430-04-20) Coarse-Grained Molecular Dynamics Simulations Evaluating Formation and Structural Stability of Nystatin-Loaded DOPC and DPPC Vesicles

Purpose: Nystatin is a BCS Class IV drug with poor solubility and permeability. DOPC (1,2-Dioleoyl-sn-glycero-3-phosphocholine) and DPPC (Dipalmitoyl phosphatidyl choline) phospholipids were used to simulate vesicular formation using Schrodinger Materials Science suite 2023-24. The potential for vesicular formation as well as the structural stability of the resulting aggregates was evaluated for each phospholipid type using the Coarse Grain (CG) Martini force field. CG models were chosen as opposed to atomistic models, as such models have lower degrees of freedom, and therefore enable longer simulations of larger systems such as liposomes and related vesicular structures.

Methods: The CG structures of DOPC and DPPC phospholipids were imported as a coarse-grained state from Materials Science 2023-4. Nystatin structure was prepared using the coarse grain sketcher (1). Simulation boxes were defined based on literature reports of sufficient molecular numbers and ratios to ensure formation of atleast one vesicle (2).  These included 901 lipids, 60311 water molecules, and 5 Nystatin molecules. The total simulation time for each phospholipid was 3000 nanoseconds (ns) with temperature 300 K, NPT ensemble class, and the time step was set at 10 femtosecond (fs).

Results: Simulations with DOPC lipids showed clear vesicular formulation, while that with DPPC lipids appeared disc-like (figure 1). DOPC vesicles showed a bilayer thickness of ~3.63 nm and vesicle radius ~ 6.40 nm, while DPPC formed a disc like bilayer structure of thickness ~ 4.62 nm. Nystatin appeared to be entrapped within the hydrophobic chains of the phospholipid membrane. At the onset of the simulation, DOPC and DPPC phospholipids were dispersed randomly and heterogeneously among water molecules. Over time, cluster formulation could be observed among the phospholipid molecules, possibly resulting from hydrophobic interactions among lipid chains. The trajectories of the lipid molecules were analyzed based on gyration radius (Rg), cluster analysis, Root mean square deviation (RMSD), Radial distribution function (RDF) and Van der Waals interaction energy analysis (figure 2). RMSD parameters for DOPC and DPPC lipids attained equilibrium at about 1 nanosecond, after which a constant value was observed ensuring stable structural formation. The number of clusters decreased from 45 and 30 to 1 for DOPC and DPPC in > 1000 ns, as phospholipid collisions resulted in the merging of clusters to make the final lipid vesicles. Aggregation to form a single large cluster of lipid vesicle was 1200 ns for the DOPC while for DPPC, it was identified as 1700 ns. The initial values of Rg were 110 nm for both DOPC and DPPC molecules, but was reduced to < 60 nm at the end of simulation. The decrease in Rg confirms the formation of elliptical and closed liposomal models with both lipids. Gyration radius of the DPPC depicted a sudden decrease, suggesting structural transformation, whereas such a sharp drop was not observed with DOPC lipids. Van der Waals interaction calculations showed that the magnitude of the energy increased substantially over the time period of the simulation. Van der Waals forces typically account for interactions between hydrophobic tails of DOPC and DPPC, causing the packing and ordering of these phospholipids to enable vesicular formation as well as their structural stabilization. The radial distribution function (RDF) confirmed that the 3000 ns time scale is appropriate for the formation and equilibration of the liposomal model for DOPC and DPPC phospholipids. The attainment of equilibrium in the lipid system is evident through the formation of stable lipid bilayers, signifying sufficient stability at this time period (3000 ns).

Conclusion: Molecular dynamics simulation demonstrated the formation of stable self-assembled vesicular structures at 3000 ns with DOPC and DPPC phospholipids, with nystatin as the model drug. The analysis of RDF, gyration radius, cluster analysis, RMSD and Vander Waals energy analysis indicates clear vesicle formation with DOPC compared to DPPC. These simulations serve as a quantitative application of mathematical principles, and provide a complementary approach for investigating the structural mechanisms and stability of lipid vesicles.

References: (1) Jaafari MR et al. Molecules. 2015 Dec 24;21(1):E6. (2) Javadi, H. & Darvishi et al. Sci Rep 2020 Feb 04; 10, 1837.


Snapshots of trajectory of simulated system containing DOPC lipid or DPPC lipid


Trajectory analysis of simulated systems containing DOPC lipid or DPPC lipid