Molecular Dynamics Simulations to Study Drug Delivery Systems

Abstract

Molecular dynamics simulation is a very powerful tool to understand biomolecular processes. In this chapter, we go over different applications of this methodology to drug delivery systems (DDS) carried out in the group. DDS-a formulation or a device that enables the introduction of a therapeutic substance in the body and improves its efficacy and safety by controlling the rate, time, and place of release of drugs-are an important component of drug development and therapeutics. Biocompatible nanoparticles are materials in the nanoscale that emerged as important players, improving efficacy of approved drugs, for example. The molecular understanding of the encapsulation process could be very helpful to guide the nanocarrier for a specific system. Here we discuss different applications of drug delivery carriers, such as liposomes, polymeric micelles, and polymersomes using atomistic and coarse grain (CG) molecular dynamics simulations.

In silico and in vitro design of cordycepin encapsulation in liposomes for colon cancer treatment

“…39 Computer simulations have been extensively used to study many biomolecular interactions such as protein-ligand interactions, protein-protein interactions and membrane transport, including drug delivery systems. [41][42][43][44][45][46] MD simulations have also been used to investigate the binding mechanisms of cordycepin and many protein targets, for example uric acid transporter 1 (URAT1) associated with anti-hyperuricemic effect 47 and Cdk-2 in cervical cancer. 48 Atomistic insight into binding properties can be used as guidance for the design of new potent proteins inhibitors.…”

Influence of Terpene Type on the Release from an O/W Nanoemulsion: Experimental and Theoretical Studies

“…The understanding of the encapsulation process on a molecular-level could be very helpful to design an effective drug carrier. Molecular dynamics (MD) simulation is a very powerful tool to understand a number of biomolecular processes and could help to develop and improve drug delivery systems [ 17 ]. MD simulations are particularly valuable in addressing issues that are difficult to explore with laboratory measurements.…”

Integrated Computational Approaches and Tools for Allosteric Drug Discovery

“…MD is an invaluable tool in the hands of protein allostery researchers [44]. MD experiments simulate biological protein movement at various levels of theory, for which molecular mechanical approximations (coupled to Newton's second law of motion) [271] are the most common for relatively large solvated protein systems. At the junction between the quantum and coarse-grained atomic models, all-atom MD simulations provide a good trade-off between accuracy and speed for conformational sampling, producing quality spatiotemporal data associated to protein action.…”