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Physical-chemical understanding of membrane partitioning and permeation at an atomic resolution : towards in silico pharmacology

Abstract : The mechanism of interaction between drugs or any xenobiotic and membrane is one of thekey factors that affect its biological of action, and so its therapeutic activity. A thoroughrationalization of the relationship between the intrinsic properties of the xenobiotics and theirmechanism of interaction with membranes can now be assessed with atomistic details.Molecular dynamics (MD) is a powerful research tool to study xenobiotics-membraneinteractions, which can access time and space scales that are not simultaneously accessibleby experimental methods. Semi-quantitative molecular and thermodynamic descriptions ofthese interactions can be provided using in silico model of lipid bilayers, often in agreementwith experimental measurements.The main goal of our investigation consisted to get in depth insight into the mechanisms ofinteraction/partitioning/insertion/crossing with/in/into/through membrane and drug deliveryusing MD. In this thesis, we have focused on both drugs used in renal transplantation (e.g.,antivirals, immunosuppressants) and antioxidants, which can also be used to protect organsalong the transplantation processes. We have provided a series of clues showing that MDsimulations can tackle the delicate process of drug passive permeation.Both, unbiased and biased MD (z-constraint) simulations have been used to elucidate thexenobiotics-membrane interactions (i.e., positioning and orientation) and to evaluate crossingenergies, diffusion coefficients, and permeability coefficients. These findings led us to drawqualitative structure-permeability relationships (SPR). We have carefully analyzed how thechemical and physical properties of xenobiotics affect the mechanism of interactions andthus permeability. The robustness of these MD-based methodologies has been determinedto qualitatively predict these pharmacological parameters. Hydrophobic compounds showeda favorable partitioning into the lipid bilayer and relatively low Gibbs energy of crossing thecenter of membrane (ΔGcross). Hydrophilic or charged compounds showed partitioning closeto membrane surface, in interaction with the polar head groups and water molecules; this hasbeen shown to dramatically increase ΔGcross. Amphiphilic compounds are intermediatecompounds in terms of membrane insertion/positioning/crossing. It clearly appears that theyshould be analyzed case by case, an analysis for which MD simulations could be particularlysupportive. Also the influence of size at predicting permeation has been studied (i.e.,relatively large drugs were tested). The molecular size has shown no significant influence onΔGcross whereas diffusion coefficients were significantly affected, depending on themembrane regions.
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Tahani Ossman. Physical-chemical understanding of membrane partitioning and permeation at an atomic resolution : towards in silico pharmacology. Human health and pathology. Université de Limoges, 2016. English. ⟨NNT : 2016LIMO0089⟩. ⟨tel-03464119⟩

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