Ye. V. Tourleigh

Computer-aided molecular design of nanocontainers for inclusion and targeted delivery of bioactive compounds

Nanotubes may serve as non-immunogenic containers of biocompounds and vehicles for selective delivery to the cell membrane. These two properties – selective inclusion and transportation – are interconnected and establish the main challenge in nanovehicle design. Molecular dynamics (MD) simulation of systems containing a carbon nanotube, water, a lipid bilayer, and a molecule to be delivered is a way to explore the problem. Absorptive properties of the nanotube were studied using the example of a pentadecapeptide and cholesterol. The uptake of these molecules turned out to be susceptible to details of the nanotube’s interfacial structure and functional groups of the molecules contacting the nanotube. Incorporation of the peptide was found to be a spontaneous process and considered as a model self-assembly of a nanodevice, further referred to as a nanosyringe. For the design of the nanosyringe the steered molecular dynamics (SMD) approach was used. Release of the peptide was performed by expulsing it through the lipid membrane. The conformational state of the peptide was studied in view of chemical stability of the substance under shock action. In principle, styling the nanotube (by adding functional groups or ligands) may achieve the selectivity of the nanotube’s landing area on the cellular membrane and implement it in drug delivery system construction.

Molecular dynamics study of molecular mobility in catenanes

Molecular machines described in this paper are meant to be such molecular systems that make use of conformational mobility (i.e. hindered rotation around chemical bonds and molecular construction deformations with formation and breakage of nonvalent bonds). Components of molecular machines move mainly by means of restricted diffusion. As an example of molecular machines of a nonbiological nature catenanes (compounds with two interlocked molecular rings) can be proposed. Thus, for example, model catenane ((2)-(cyclo-bi (paraquat-p-phenylene))- (1(2,6)-tetrathiafulvalena-16(1,5)naphtalena-3, 6, 9, 12, 15, 17, 20, 23, 26, 29- decaoxatnacontaphane)-catenane) changes its redox status when an electric field is applied, and rotation of the rings takes place. It occurs with fixation at certain moments of the influence. To find out characteristic properties of rings movements under various external conditions molecular dynamics simulation was carried out. Three cationic forms of the catenane were first subjected to geometrical optimization and quantum chemical calculation.

Comparative Study of Molecular Dynamics, Diffusion, and Permeability for Ligands in Biomembranes of Different Lipid Composition

A comparative study of several model lipid bilayers of different composition, which included analysis of kinetic parameters of model lipid bilayers and permeability of bilayer membranes for small molecules, has been carried out. The conformity of results of numeric experiments to experimental data (structure of membrane lipid bilayers, lateral diffusion coefficients, and relative permeability of biomembranes for ligands) is discussed in the framework of a standard molecular dynamics protocol.

Diffusion of Molecules at the Interface of Water-Membrane Structures

The distributions and transfer energies of several molecules and atomic groups between water and a structured hydrophobic phase were calculated by the molecular dynamics method. The coefficients of oxygen diffusion in a tetradecane membrane were estimated. The transfer energy of charged atomic groups was found to correlate with changes in the Born solvation energy. The contributions of atoms to the transfer energy of functional groups were shown to be non-additive. The steered dynamics method for estimating the kinetic parameters of the penetration of molecules through interphase boundaries was developed. Heterogeneous microviscosity of a membrane was calculated for a hydrated l-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine bilayer. Effects of the chemical properties of penetrant molecule on its translocation through the membrane were studied.