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In this study, molecular dynamics simulation is applied to investigate drug transport in both pure state and conjugated with neutral gold nanoparticle (AuNP) as a drug carrier inside dipalmitoylphosphatidylcholine (DPPC) membrane. Flutamide (Flu) as a hydrophobic and Glutathione (GSH) as a hydrophilic anticancer drug are selected as the case studies. Dynamics of each drug including adhesion on and penetration into the cell membrane are investigated. Pure and conjugated form of drugs inside the water and near the membrane are studied. Simulation results show that the interaction between drug molecules and DPPC changes after drug conjugating with AuNP. GSH, as a hydrophilic drug, intends to remain above the membrane bilayer and after conjugating with AuNP diffuses inside DPPC. However, hydrophobic Flu molecule likes to diffuse inside DPPC, but after conjugating with AuNP, its diffusion inside the lipid bilayer decreases, and its retention time at the surface of DPPC increases. Presence of Flu-NP at the surface of DPPC could enhance its impact on blocking dihydrotestosterone binding at androgen receptors resulting in tumor cell growth arrest. In addition, the tendency of GSH-NP for diffusion to the DPPC is a positive factor for the successful transport of heavy metals such as AuNP without rapid clearance through either the hepatobiliary pathway or the renal system. In conclusion, such MD simulation results may solve problems in nanomedicine translation and turn into a bridge toward maximizing targeting and minimizing nanotoxicity of metal NPs. [Display omitted] • Atomistic MD simulation was performed for drug transport inside DPPC membrane. • Gold nanoparticle was selected as a drug carrier. • Flutamide and Glutathione were selected as hydrophobic/hydrophilic anticancer drugs. • AuNP changed mechanism of drug interaction with LBL at pure and conjugated states. • Drug conjugated with NP enters from its NP side chain inside lipid bilayer. [ABSTRACT FROM AUTHOR]