Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

Rózsa, Zsófia Borbála; Németh, Lukács; Jójárt, Balázs; Nehéz, Károly; Viskolcz, Béla; Szőri, Milán

doi:10.1021/acs.jpcb.9b04313

Cited by 8 publications

(8 citation statements)

References 120 publications

(256 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Antiseptic Picloxydine, Octenidine, Miramistin [470], Polyhexamethylene Biguanide [471] Insecticide Parathione [132], Fipronil [472], Dibutyl succinate [203] Former Drugs d-sotalol, cisapride [473], piracetam (status varies among countries) [474], ORG-12962 [199] Toxic xenobiotic Polybrominated-diphenyl-ethers [475], Bisphenol [476], Perfluoroalkyls [477], nitroaromatic explosives (TNT,2A, and 24DA) [478][479][480][481], 1,4-Dioxane [482], Benzo[a]pyrene [483] Nanomaterials Graphene [484][485][486][487], Carbon Dots [488], Phosphorene Oxide Nanosheets [489], Gold Nanoparticles [490][491][492], Titanium Dioxide Nanoparticles [493], Generic Nanoparticles (coarse grained) [494], Fullerene [495][496][497][498], Previous reviews [499] Polymers Poly(ethyleneoxide)-Poly-(propylene oxide) [500], polyethylenimine [501], Poloxamer [502,503], Pluronics [504,505], poly(ethyleneglycol)-desferrioxamine/ gallium [506], PEG functionalized with carbochydrates [507] and peptides…”

Section: Application Xenobioticmentioning

confidence: 99%

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

2021

View full text Add to dashboard Cite

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard “lock and key” paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

show abstract

Section: Application Xenobioticmentioning

confidence: 99%

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

2021

View full text Add to dashboard Cite

show abstract

“…Strong VdW repulsion is responsible for the severe free-energy alteration close to the clay surface. The results illustrate the similarity between the sites of the free-energy minima for the 6 phthalates, implying the presence of preferred adsorption regions on the clay surface (a) 59. The free-energy alteration of 1,4-dioxane penetration into a DPPC bilayer along the Z-axis is illustrated 60.…”

mentioning

confidence: 67%

“…The results illustrate the similarity between the sites of the free-energy minima for the 6 phthalates, implying the presence of preferred adsorption regions on the clay surface (a). 59 The free-energy alteration of 1,4-dioxane penetration into a DPPC bilayer along the Z-axis is illustrated. 60 The black curve depicts the outputs of metadynamics simulations for a system containing 100 molecules of 1,4-dioxane, whereas the red curve depicts a dioxane concentration of 7.510 g/dm 3 configuration during the simulation can be recognized.…”

Section: Pollutant Adsorption Intensity and Stabilitymentioning

confidence: 99%

“…Calculating adsorption-free energy and adsorption energy is an efficient method for determining if an adsorption process is thermodynamically advantageous. 59 Free-energy profiles can determine the partitioning and the adsorbate molecule position during processes like membrane penetration and adsorption using soil clay minerals or for pore structure adsorbents such as zeolite. However, during such phenomena, a high energy barrier exists.…”

Section: Pollutant Adsorption Intensity and Stabilitymentioning

confidence: 99%

Section: Adsorption Mechanismmentioning

confidence: 99%

See 2 more Smart Citations

Elucidating the Sorption Mechanisms of Environmental Pollutants Using Molecular Simulation

Mousavi

Shadman

Habibi

et al. 2023

Ind. Eng. Chem. Res.

View full text Add to dashboard Cite

With the global expansion of industrial activities, the entry of various pollutants into the environment has remained a serious issue. One of the best ways to remove these pollutants is to use the adsorption method. Understanding adsorption mechanisms to improve and optimize adsorbents are pivotal for adsorbent development. In this study, the application of molecular simulation in developing various adsorbents has been reviewed. A variety of molecular simulation methods such as molecular dynamics (MD), density functional theory (DFT), hybrid quantum and classical molecular dynamics (QM/MM), ab initio molecular dynamics (AIMD), and coarse-grained molecular dynamics have been used to study these processes. Although hardware limitations prevented researchers from using this method for real systems, this problem has been solved thanks to the development of computing power units (CPUs) and graphic processing units (GPUs). Due to the increasing use of molecular simulations, an attempt has been made to review previous work in this field. Investigations were conducted on various capabilities of molecular simulations in studying the adsorption process and its limitations. In addition to lowering the cost and time of industrial research, this study advances molecular simulations in academic studies. These simulations can reveal the mechanisms underlying adsorption and the selection, development, and design of suitable adsorbents and adsorption processes. Although investigating the adsorption mechanisms for the selection and design of the process is a complicated problem, this work tends to shed light on almost all types of molecular simulations and their applications in studying the adsorption process of removing various environmental pollutants by various adsorbents.

show abstract

Chemical space of the singlet C4H8O2 species. A systematic theoretical analysis on their structural and thermochemical properties

Rózsa

Rágyanszki

Viskolcz

et al. 2023

Computational and Theoretical Chemistry

View full text Add to dashboard Cite

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

Cited by 8 publications

References 120 publications

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

Elucidating the Sorption Mechanisms of Environmental Pollutants Using Molecular Simulation

Chemical space of the singlet C4H8O2 species. A systematic theoretical analysis on their structural and thermochemical properties

Contact Info

Product

Resources

About