Molecular dynamics simulations of doxorubicin in sphingomyelin-based lipid membranes

An in Silico Approach to Reveal the Nanodisc Formulation of Doxorubicin

“…Such amphiphilic characteristics of DOX may enable rapid membrane penetration and diffusion (Toroz and Gould, 2019). The stability of DOX binding modes to the ND membrane could be dependent on lipid composition (Siani et al, 2022). Through the comparison between three types of ND formulations of lipidated-DOX prodrugs, we observed that lipidation approaches could provide sufficient conformational stability for prodrug loading and different lipid used for lipidation led to variable loading capacity.…”

Multi-scale modeling of folic acid-functionalized TiO2nanoparticles for active targeting of tumor cells

“…52 The mean force, 〈 F ξ 〉 ξ , exerted along the transition coordinate, ξ , is related to the free energy first derivative according to:where | J | is the Jacobian determinant to transform the Cartesian coordinates to generalized coordinates and 〈 F ξ 〉 ξ denotes the cumulative mean of the instantaneous force, F ξ , in bins δ ξ wide. To obtain the free energy profiles, we followed a protocol similar to that of a previous work by some of us: 53 the reaction coordinate, defined as the z -component of the distance between the center of mass of the FA molecule and the center of the NP, was discretized into six consecutive windows, each 5 Å wide, at a z -distance from 10 to 40 Å with respect to NP center. To keep the FA molecule at the desired z -distance from the center of the NP, its center of mass was harmonically restrained in both the window's edges and the xy plane perpendicular to the transition coordinate with a force constant of 10 kcal mol −1 Å −2 .…”

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

“…Shobhna, Kumari, and Kashyap found that ionic liquids increase membrane condensing using simulations . Siani et al studied doxorubicin, a widely used cancer treatment drug, in sphingomyelin-based membranes in order to optimize the liposome-based drug delivery for doxorubicin . Kneiszl, Hossain, and Larsson studied how intestinal permeation enhancers interact with membranes to lay the basis for improving the efficacy of oral administration drugs .…”

“…A plethora of publications has examined the membrane interactions with a variety of compounds, including psilocin (active hallucinogen of magic mushrooms), ionic liquids, , cancer drugs, DNA transfection reagent, and dye probes. − Ionic liquids are liquid salts consisting of organic cations and inorganic anions and are considered a green alternative to organic solvents . Shobhna, Kumari, and Kashyap found that ionic liquids increase membrane condensing using simulations .…”

“…274 Siani et al studied doxorubicin, a widely used cancer treatment drug, in sphingomyelinbased membranes in order to optimize the liposome-based drug delivery for doxorubicin. 275 Kneiszl, Hossain, and Larsson studied how intestinal permeation enhancers interact with membranes to lay the basis for improving the efficacy of oral administration drugs. 280 Sabin et al studied polyethylenimine and its interactions with membranes using simulations and showed that polyethylenimine induces pore-forming in the membrane, contributing to an understanding of the DNA cell transfection process.…”