Molecular dynamics simulations of Oxprenolol and Propranolol in a DPPC lipid bilayer

De novo antioxidant peptide design via machine learning and DFT studies

Antioxidant peptides (AOPs) are highly valued in food and pharmaceutical industries due to their significant role in human function. This study introduces a novel approach to identifying robust AOPs using a deep generative model based on sequence representation. Through filtration with a deep-learning classification model and subsequent clustering via the Butina cluster algorithm, twelve peptides (GP1-GP12) with potential antioxidant capacity were predicted. Density functional theory (DFT) calculations guided the selection of six peptides for synthesis and biological experiments. Molecular orbital representations revealed that the HOMO for these peptides is primarily localized on the indole segment, underscoring its pivotal role in antioxidant activity. All six synthesized peptides exhibited antioxidant activity in the DPPH assay, while the hydroxyl radical test showed suboptimal results. A hemolysis assay confirmed the non-hemolytic nature of the generated peptides. Additionally, an in silico investigation explored the potential inhibitory interaction between the peptides and the Keap1 protein. Analysis revealed that ligands GP3, GP4, and GP12 induced significant structural changes in proteins, affecting their stability and flexibility. These findings highlight the capability of machine learning approaches in generating novel antioxidant peptides.

Elucidating anticancer drugs release from UiO-66 as a carrier through the computational approaches

The computational analysis of drug release from metal-organic frameworks (MOFs), specifically UiO-66, is the primary focus of this research. MOFs are recognized as nanocarriers due to their crystalline structure, porosity, and potential for added functionalities. The research examines the release patterns of three drugs: temozolomide, alendronate, and 5-fluorouracil, assessing various factors such as the drugs' distance from the UiO-66 centers, the interaction of drug functional groups with Zr metal ions, and the drug density throughout the nanocarrier. Findings reveal that 5-fluorouracil is located furthest from the UiO-66 center and exhibits the highest positive energy compared to the other drugs. Alendronate's density is observed to shift to the carrier surface, while 5-fluorouracil's density significantly decreases within the system. The drug density diminishes as the distance from the UiO-66 center of mass increases, suggesting a stronger positive interaction between the drugs and the nanocarrier. Moreover, Monte Carlo calculations were employed to load drugs onto the UiO-66 surface, leading to a substantial release of 5-fluorouracil from UiO-66. Quantum and Monte Carlo adsorption localization calculations were also conducted to gather data on the compounds' energy and geometry. This research underscores the potential of MOFs as nanocarriers for drug delivery and highlights the crucial role of temperature in regulating drug release from UiO-66. It provides insights into the complex dynamics of drug release and the factors influencing it, thereby emphasizing the promise of UiO-66 as a viable candidate for drug delivery. This work contributes to our understanding of UiO-66's role and sets the stage for improved performance optimization in the cancer treatment.

Effect of liposome composition on β-blocker interactions studied by capillary electrokinetic chromatography

Liposome capillary electrokinetic chromatography was used to investigate the interactions between three β-blockers of different hydrophobicity and various liposome solutions. The studied β-blockers comprised alprenolol, propranolol, and carvedilol. The composition of the liposome solutions, containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1,2-dioleoyl-sn-glycero-3-phos-phoethanolamine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine, and cholesterol in various molar ratios, was designed by a response surface methodology-central composite design approach. Subsequently, after conducting the liposome capillary electrokinetic chromatography experiments and determining the retention factors from the electrophoretic mobilities of the compounds, and further calculating the distribution coefficients, an analysis of variance was performed. After extracting the statistical models, optimal operational conditions were obtained based on the developed models. To further investigate the interactions between the β-blockers and the liposomes, nanoplasmonic sensing experiments were carried out on two different liposome systems. The overall results demonstrate the strong influence of cholesterol and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine on the distribution coefficients.

The effects of adsorbed benzo(a)pyrene on dynamic behavior of polystyrene nanoplastics through phospholipid membrane: A molecular simulation study

Nanoplastics (NPs) are mainly generated from the decomposition of plastic waste and industrial production, which have attracted much attention due to the potential risk for humans. The ability of NPs to penetrate different biological barriers has been proved, but the understanding of molecular details is very limited, especially for organic pollutant-NP combinations. Here, we investigated the uptake process of polystyrene NPs (PSNPs) combined with benzo(a)pyrene (BAP) molecules by dipalmitoylphosphatidylcholine (DPPC) bilayers by molecular dynamics (MD) simulations. The results showed that the PSNPs can adsorb and accumulate BAP molecules in water phase and then carried BAP molecules to enter DPPC bilayers. At the same time, the adsorbed BAP promoted the penetration of PSNPs into DPPC bilayers effectively by hydrophobic effect. The process of BAP-PSNP combinations penetrating into DPPC bilayers can be summarized into four steps including adhesion on the DPPC bilayer surface, uptake by the DPPC bilayer, BAP molecules detached from the PSNPs, and the PSNPs depolymerized in the bilayer interior. Furthermore, the amount of adsorbed BAP on PSNPs affected the properties of DPPC bilayers directly, especially the fluidity of DPPC bilayers that determine the physiologic function. Obviously, the combined effect of PSNPs and BAP enhanced the cytotoxicity. This work not only presented a vivid transmembrane process of BAP-PSNP combinations and revealed the nature of the effects of adsorbed benzo(a)pyrene on the dynamic behavior of polystyrene nanoplastics through phospholipid membrane, but also provide some necessary information of the potential damage for organic pollutant-nanoplastic combinations on human health at a molecular level.

Propranolol induces large-scale remodeling of lipid bilayers: tubules, patches, and holes

Herein, we report fluorescence microscopy analysis of the interaction between propranolol (PPN), a beta-adrenergic blocking agent, and planar supported lipid bilayers (SLBs), as model membranes. The results indicate that PPN can remarkably promote largescale remodeling in SLBs with various lipid compositions. It was found that PPN insertion induces the formation of long microtubules that can retract into hemispherical caps on the surface of the bilayer. These transformations are dynamic, partially reversible, and dependent upon the drug concentration. Quantitative analysis revealed a three-step model for PPN-lipid bilayer interaction, with the first step involving interfacial electrostatic adsorption, the second step centered on hydrophobic insertion, and the third step associated with membrane disruption and hole formation. By introducing cholesterol, phosphoethanolamine, phosphatidylglycerol, and phosphatidylserine lipids into the phosphocholine SLBs, it was illustrated that both the chemistry of the lipid headgroups and the packing of lipid acyl chains can substantially affect the particular steps in the interactions between PPN and lipid bilayers. Our findings may help to elucidate the possible mechanisms of PPN interaction with lipid membranes, the toxic behavior and overdosage scenarios of beta-blockers, and provide valuable information for drug development and modification.

Mechanism of interactions between tripeptide NCW on cellular membrane using molecular dynamic simulation

Tripeptide NCW identified in Mizuhopecten yessoensis has been shown to possess in vivo antihypertensive effect. However, the poor understanding of the absorption of NCW across the membrane limits its application. In this study, we have investigated the interaction of NCW with DPPC membrane via 400 ns all-atom molecular dynamic simulation using GROMACS software. The structural variations of NCW during absorption, the location and distribution of NCW in the membrane, and the effect of NCW on the properties of membranes during simulation were analyzed to understand the dynamic behavior of NCW in DPPC membrane system. The results suggested that the structures of NCW were stable during simulation. Further, NCW could bind on the surface of the DPPC membrane and enter the hydrophobic interior of the DPPC membrane. Residue Try played an important role in the absorption of NCW across the membrane. Hydrogen bonds and hydrophobic interactions stabilized the interaction of NCW with the membrane. All the above studies analyzed the interaction mechanism between NCW and DPPC membranes at the atomic level and laid the foundation for further transmembrane studies of NCW.

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.