Computational protocol: Influence of doxorubicin on model cell membrane properties: insights from in vitro and in silico studies

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Protocol publication

[…] All-atom molecular dynamics simulations of doxorubicin molecule were performed with 2 membrane bilayers, with the following lipid compositions, DMPC:SM [8:2] DMPC:SM:Chol [7:1.5:1.5]. For lipid molecules S-lipids forcefield parameters were used–. For water molecules we used the TIP3P model compatible with the S-lipids forcefield set. Periodic boundary conditions with minimum image convention were used in all directions. Covalent bond lengths were preserved through the linear constraint solver (LINCS) algorithm. For all systems the temperature was controlled using the Nosé-Hoover thermostat with solvent and solute controlled independently, . Pressure was controlled using the Parrinello-Rahmann barostat with semi-isotropic control. Lennard-Jones interactions were cut off at 1.4 nm and for the electrostatic interactions the particle mesh Ewald method (PME) was used. For all simulations physiological pressure and temperature were used (1 Bar and 37 °C). The GROMACS open source software package, version 4.6.5, was used for all Molecular Dynamics (MD) simulations, along with all quantitative analysis. Visualization of the trajectories was performed using the Visual Molecular Dynamics (VMD) package. For doxorubicin, the partial charges were derived with RESP procedure implemented in ANTECHAMBER. All the simulation systems were simulated for 1.2 microsecond. The first 200 ns were considered as an equilibration phase and, hence all the analysis was performed on the latter 1 microsecond trajectories. [...] Statistical analysis was performed using IBM® SPSS® Statistics software (v., IBM, Armonk, NY, USA). The measurements were repeated at least three times and data was expressed as mean ± standard deviation (SD). Data was statistically analyzed through the one-way analysis of variance (ANOVA) method and differences between groups were compared by Bonferroni and Tukey post-hoc tests in which a p value lower than 0.05 (p < 0.05) was considered statistically significant. […]

Pipeline specifications

Software tools GROMACS, VMD, SPSS
Applications Miscellaneous, Protein structure analysis
Chemicals Cholesterol, Doxorubicin