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WIREs Comput Mol Sci
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Molecular simulations in drug delivery: Opportunities and challenges

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Molecular simulations are promising tools for in silico design of drug delivery formulations, as they provide a prediction of formulation properties prior to synthesis thus minimizing the need for in vitro and in vivo experimentation. The detailed molecular insight obtained by these simulations is precious and often beyond the reach of sophisticated experimental facilities. Although initially limited to the prediction of single‐molecule behavior (e.g., drug orientation in a bilayer), gradual advances in computing speed and efficient simulation approaches have made it feasible to employ these methods for phenomena occurring at substantially large length and time scales (e.g., carrier‐drug complexation) with modest computational cost and resources. We present a nonmathematical review of molecular simulation methods and their applications in drug delivery, with special emphasis on the use of atomistic and coarse‐grained Monte Carlo (MC) and molecular dynamics (MD) methods and excluding the drug docking studies used in drug discovery. Current capabilities and problems associated with the use of these methods in the context of drug delivery are highlighted, along with a discussion of representative applications of molecular simulations in drug delivery. We conclude that while molecular simulations are expected to play a central role in the future of drug delivery field, we require a concerted effort of computational scientists, experimentalists, and industry personnel working on drug delivery to identify specific areas where these simulations can be especially useful. This article is categorized under: Structure and Mechanism > Computational Materials Science Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Software > Molecular Modeling
Basic steps of atomistic (Monte Carlo (MC)/molecular dynamics (MD)) simulations
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Thermodynamic cycle used in the calculation of binding free energy
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Two‐dimensional representation of periodic boundary condition. The central cell (filled with yellow) represents the simulation box. Filled circles represent particles in the simulation box and open circles represent their periodic image in other cells. Bold and dashed lines shows movement of two particles near the boundary; as a particle leaves the simulation box, its image enters the box from the opposite end
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(a) and (b) shows the atomistic representation of a model polymeric drug‐carrier syndiotactic polyacrylic acid chain containing 20 repeat units (PAA20) and a model anticancer drug doxorubicin (DOX), respectively. Here, carbon, hydrogen, oxygen, and nitrogen atoms are shown in gray, white, red, and blue colors, respectively. Figure2(c) and (d) shows initial simulation configuration of a single DOX molecule in water and a DOX molecule along with a PAA20 molecule in cubic simulation box of length 6 nm, respectively. Periodic boundary conditions (PBCs) are used at all faces of the simulation box. Figure (e) and (f) shows initial simulation configuration of multiple DOX molecules in water and multiple DOX molecule along with multiple PAA20 molecules, respectively. In Figure (c)–(f), DOX, PAA20, and water molecules are shown in green, red, and cyan colors, respectively. Figure (g) shows a coarse‐grained (CG) representation of PAA20 with the circles representing coarse‐grained beads
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Software > Molecular Modeling
Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Structure and Mechanism > Computational Materials Science

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