Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations

Efficacy of analgesia promoted by lidocaine and articaine in third molar extraction surgery. A split-mouth, randomized, controlled trial

PURPOSE

The aim of this study was to compare the analgesic efficacy of 4% articaine associated with epinephrine (1:100,000), and 2% lidocaine associated with epinephrine (1:100,000) in third molar extraction surgery.

METHODS

Sixty patients who underwent surgeries to extract upper and lower third molars were included in this split-mouth, double-blind, randomized, controlled trial. The groups in this study were divided according to the anesthetic solution used to provide local anesthesia during extraction of upper and lower third molars: (1) 4% articaine associated with epinephrine (1:100,000); (2) 2% lidocaine associated with epinephrine (1:100,000). The time to the beginning and end of the sensation of analgesia, pain sensation according to the VAS scale, and number of anesthetic tubes necessary for supplementation were analyzed.

RESULTS

It was found that the onset time for analgesia was shorter on the side anesthetized with articaine compared to the side anesthetized with lidocaine (122.1 ± 52.90 s vs. 144.5 ± 68.85 s) (p < 0.05). In addition, the number of tubes used for anesthetic supplementation was also reduced on the articaine side compared to the lidocaine side (0.26 ± 0.48 vs. 0.50 ± 0.75) (p < 0.05). There were no differences between the anesthetic solutions in the other evaluated parameters.

CONCLUSION

It can be concluded that the use of 4% articaine associated with epinephrine (1:100,000) reduced the time of onset of analgesia and the necessity for anesthetic supplementation in third molar extraction surgeries compared to the use of 2% lidocaine associated with epinephrine (1:100,000).

Modulation of Phospholipase A2 Membrane Activity by Anti-inflammatory Drugs

The phospholipase A2 (PLA2) superfamily consists of lipolytic enzymes that hydrolyze specific cell membrane phospholipids and have long been considered a central hub of biosynthetic pathways, where their lipid metabolites exert a variety of physiological roles. A misregulated PLA2 activity is associated with mainly inflammatory-derived pathologies and thus has shown relevant therapeutic potential. Many natural and synthetic anti-inflammatory drugs (AIDs) have been proposed as direct modulators of PLA2 activity. However, despite the specific chemical properties that these drugs share in common, little is known about the indirect modulation able to finely tune membrane structural changes at the precise lipid-binding site. Here, we use a novel experimental strategy based on differential scanning calorimetry to systematically study the structural properties of lipid membrane systems during PLA2 cleavage and under the influence of several AIDs. For a better understanding of the AIDs-membrane interaction, we present a comprehensive and comparative set of molecular dynamics (MD) simulations. Our thermodynamic results clearly demonstrate that PLA2 cleavage is hindered by those AIDs that significantly reduce the lipid membrane cooperativity, while the rest of the AIDs oppositely tend to catalyze PLA2 activity to different extents. On the other hand, our MD simulations support experimental results by providing atomistic details on the binding, insertion, and dynamics of each AID on a pure lipid system; the drug efficacy to impact membrane cooperativity is related to the lipid order perturbation. This work suggests a membrane-based mechanism of action for diverse AIDs against PLA2 activity and provides relevant clues that must be considered in its modulation.

Protonation and orientation: a computational approach to cocaine diffusion through a model membrane

We study the diffusion of cocaine through a DMPC lipid bilayer as an example of a protonable, amphiphilic molecule passing a biological membrane. Using classical molecular dynamics simulations, the free...

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

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.

Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations

Previous studies suggested that naturally occurring EGCG primarily acted on the bacterial cell membrane then damaged the membrane and the gallate moiety in EGCG was very important to its anti-bacterial activity. However, the detailed mechanisms were still poorly understood. In this paper, EGCG and EGC were selected to study the great contribution of gallate moiety on the anti-bacterial activities of polyphenols. The results indicated that EGCG could penetrate deeper into the POPG lipid bilayer and possess more potent structure-perturbing potency on the POPG lipid bilayer than EGC. We also found that EGCG had the ability to form hydrogen bonds with the deeper inside oxygen atoms in the POPG lipid bilayer and the gallate moiety was the key functional group for EGCG forming hydrogen bonds with the POPG lipid bilayer. Moreover, results from the binding free energy analysis demonstrated that the gallate moiety made great contribution to the high affinity between EGCG and the POPG lipid bilayer. We believed that these findings could yield useful insights into the influence mechanisms of gallate moiety on the anti-bacterial activities of polyphenols.

Permeation of Biopolymers Across the Cell Membrane: A Computational Comparative Study on Polylactic Acid and Polyhydroxyalkanoate

Polymeric nanoparticles, which by virtue of their size (1-1000 nm) are able to penetrate even into cells, are attracting increasing interest in the emerging field of nanomedicine, as devices for, e.g., drugs or vaccines delivery. Because of the involved dimensional scale in the nanoparticle/cell membrane interactions, modeling approaches at molecular level are the natural choice in order to understand the impact of nanoparticle formulation on cellular uptake mechanisms. In this work, the passive permeation across cell membrane of oligomers made of two employed polymers in the biomedical field [poly-D,L-lactic acid (PDLA) and poly(3-hydroxydecanoate) (P3HD)] is investigated at fundamental atomic scale through molecular dynamics simulations. The free energy profile related to membrane crossing is computed adopting umbrella sampling. Passive permeation is also investigated using a coarse-grained model with MARTINI force field, adopting well-tempered metadynamics. Simulation results showed that P3HD permeation is favored with respect to PDLA by virtue of its higher hydrophobicity. The free energy profiles obtained at full atomistic and coarse-grained scale are in good agreement each for P3HD, while only a qualitative agreement was obtained for PDLA. Results suggest that a reparameterization of non-bonded interactions of the adopted MARTINI beads for the oligomer is needed in order to obtain a better agreement with more accurate simulations at atomic scale.

Metadynamics to Enhance Sampling in Biomolecular Simulations

Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.

Molecular dynamics simulation study of the effect of halothane on mixed DPPC/DPPE phospholipid membranes

We report results of a molecular dynamics simulation study of the effect of one general anesthetic, halothane, on some properties of mixed DPPC/DPPE phospholipid membranes. This is a suitable model for the study of simple, two-phospholipid membrane systems. From the simulation runs, we determined several membrane properties for five different molecular proportions of DPPC/DPPE. The effect of halothane on the studied membrane properties (area per lipid molecule, density of membrane, order parameter, etc.) was rather small. The distribution of halothane is not uniform through the bilayer thickness. Instead, there is a maximum of anesthetic concentration around 1.2 nm from the center of the membrane. The anesthetic molecule is located close to the phospholipid headgroups. The position of the halothane density maximum depends slightly on the DPPC/DPPE molar proportion. Snapshots taken over the plane of the membrane, as well as calculated two-dimensional radial distribution functions show that the anesthetic has no preference for either phospholipid (DPPC or DPPE). Our results indicate that this anesthetic molecule has only small effects on DPPC/DPPE mixed membranes. In addition, halothane displays no preferential location around DPPC or DPPE. This is probably due to the hydrophobic nature of halothane and to the fact that the chosen phospholipids have the same hydrophobic tails.

Quantum chemical and molecular dynamics modelling of hydroxylated polybrominated diphenyl ethers

A series of 19 hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been studied using density functional theory (DFT) and molecular dynamics simulations with the purpose of investigating eventual correlations between their physicochemical properties and toxic action. Dissociation constants (pK_a), solvation free energies and octanol-water partition coefficients (log P) have been computed. Additionally, metadynamics simulations of OH-PBDEs passing through a lipid bilayer have been carried out for four OH-PBDE species. No correlations between computed pK_a values and toxicity data have been found. Medium correlations were found between partition coefficients and the ability of OH-PBDEs to alter membrane potential in cell cultures, which is attributed to higher uptake of molecules with larger log P parameters. It was also demonstrated that in lipid bilayers, OH-PBDE molecules differ in their orientational distributions and can adopt different conformations which can affect the uptake of these molecules and influence the pathways of their toxic action.