Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: a molecular dynamics simulation approach

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).

Molecular dynamics simulation study of doxorubicin adsorption on functionalized carbon nanotubes with folic acid and tryptophan

In this work, molecular dynamics (MD) simulation is used to study the adsorption of the anticancer drug, doxorubicin (DOX), on the wall or surface of pristine and functionalized carbon nanotubes (FCNTs) in an aqueous solution. Initially, the CNTs were functionalized by tryptophan (Trp) and folic acid (FA), and then the DOX molecules were added to the system. The simulation results showed that the drug molecules can intensely interact with the FCNTs at physiological pH. Furthermore, it was found that as a result of functionalization, the solubility of FCNTs in an aqueous solution increases significantly. The effect of pH variation on drug release from both pristine and FCNTs was also investigated. The obtained results indicated that in acidic environments due to protonation of functional groups (Trp) and as a result of repulsive interaction between the DOX molecule and functional groups, the release of DOX molecules from FCNT’s surface is facilitated. The drug release is also strongly dependent on the pH and protonated state of DOX and FCNT.

CellSys: An open-source tool for building initial structures for bio-membranes and drug-delivery systems

Since phospholipids are the most important components in the structure of biomembranes, they deserve to be considered with a lot of attention in both experimental and computational theoretical studies using molecular simulation methods related to the research in the fields of drug design and drug delivery where they involve knowledge about the interactions of drug molecules with cell membranes. To employ the molecular simulation approach for this purpose the essential requirement is having information about the initial structure of phospholipids and how they interact with the drugs. Therefore in this article, we introduce an open-source software package in Python programming language for utilizing data manipulation for generation and developing the initial structure of biomolecular cells to provide the needed information for investigation in drug delivery systems. In addition, the proposed software package can be used for the efficient storage of membrane structural data to be exploited in designing new drug delivery systems. To verify the performance of the code and the results of the simulations, several analyses have been done, such as the calculation of area per lipid and self-diffusion coefficient, in addition to lipid order parameter. The results were in complete agreement with the references.

Molecular Dynamics Assessment of Doxorubicin Adsorption on Surface-Modified Boron Nitride Nanotubes (BNNTs)

Loading therapeutic agents on nanocarriers in order to protect them during drug delivery and exclusively targeting damaged tissues has gained substantial significance in biology realms in the past decade. Boron nitride nanotubes have given a new lease on designing nano delivery systems by virtue of their unique properties. The studies are still ongoing to thoroughly identify their chemical characteristics. In this study, we probed into the efficacy of boron nitride nanotubes and the impact of their surface modification by hydroxyl and amine functional groups in interaction with an anticancer drug model, i.e., doxorubicin. Defining the altered electronic properties of the nanotubes as well as the distribution of partial charges were carried out through density functional theory calculations, following the simulation of the drug loading process via molecular dynamics algorithms. The primary outcomes are inferred from systematical energies, van der Waals and electrostatic interactions, radial distribution functions, the number of hydrogen bonds, mean square displacement, diffusion coefficients, and binding free energies. Negative values of van der Waals energies imply a rapid, exothermic adsorption process whereby the contribution of these driving forces is more dominant than electrostatic ones. Ultimately, the values of overall diffusion coefficients of drugs and binding free energies, performed by the MM/PBSA approach, corroborate that the hydroxyl and amine-functionalized nanotubes reinforce the binding strength of the complexes to an approximate extent.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

Adsorption and encapsulation of the drug doxorubicin on covalent functionalized carbon nanotubes: A scrutinized study by using molecular dynamics simulation and quantum mechanics calculation

Adsorption of the drug doxorubicin (DOX) onto covalent functionalized carbon nanotubes (CNTs) as drug carriers was studied by employing molecular dynamics (MD) simulation. CNT was covalently functionalized by the chemical groups: amine, carboxyl and hydroxyl and the change in the electrostatic charge of CNT as a result of functionalization was investigated by quantum mechanics calculations. The drug adsorption onto the functionalized CNTs (f-CNT) was examined by analyzing the evaluated radial probability of the drug by MD simulation. Overall consideration of the results demonstrated that surface functionalization enhances the loading capacity of CNT for the drug encapsulation, also agglomeration of unprotonated drug molecules has increased encapsulation capacity. Analysis of the obtained results indicated that carboxyl and amine f-CNTs can act as a pH sensitive drug carrier where their protonation in acidic condition can decrease the electrostatic interactions of the loaded drug with the f-CNT and as a result can promote the drug release.

Effect of drug amlodipine on the charged lipid bilayer cell membranes DMPS and DMPS + DMPC: a molecular dynamics simulation study

In this work, the effects of the anti-hypertensive drug amlodipine in native and PEGylated forms on the malfunctioning of negatively charged lipid bilayer cell membranes constructed from DMPS or DMPS + DMPC were studied by molecular dynamics simulation. The obtained results indicate that amlodipine alone aggregates and as a result its diffusion into the membrane is retarded. In addition, due to their large size aggregates of the drug can damage the cell, rupturing the cell membrane. It is shown that PEGylation of amlodipine prevents this aggregation and facilitates its diffusion into the lipid membrane. The interaction of the drug with negatively charged membranes in the presence of an aqueous solution of NaCl, as the medium, is investigated and its effects on the membrane are considered by evaluating the structural properties of the membrane such as area per lipid, thickness, lipid chain order and electrostatic potential difference between bulk solution and lipid bilayer surface. The effect of these parameters on the diffusion of the drug into the cell is critically examined and discussed.

In silico pharmacology: Drug membrane partitioning and crossing

Over the past decade, molecular dynamics (MD) simulations have become particularly powerful to rationalize drug insertion and partitioning in lipid bilayers. MD simulations efficiently support experimental evidences, with a comprehensive understanding of molecular interactions driving insertion and crossing. Prediction of drug partitioning is discussed with respect to drug families (anesthetics; β-blockers; non-steroidal anti-inflammatory drugs; antioxidants; antiviral drugs; antimicrobial peptides). To accurately evaluate passive permeation coefficients turned out to be a complex theoretical challenge; however the recent methodological developments based on biased MD simulations are particularly promising. Particular attention is paid to membrane composition (e.g., presence of cholesterol), which influences drug partitioning and permeation. Recent studies concerning in silico models of membrane proteins involved in drug transport (influx and efflux) are also reported here. These studies have allowed gaining insight in drug efflux by, e.g., ABC transporters at an atomic resolution, explicitly accounting for the mandatory forces induced by the surrounded lipid bilayer. Large-scale conformational changes were thoroughly analyzed.