Phytochemicals in Pancreatic Cancer Treatment: A Machine Learning Study.

The discovery of new strategies and novel therapeutic agents is crucial to improving the current treatment methods and increasing the efficacy of cancer therapy. Phytochemicals, naturally occurring bioactive constituents derived from plants, have great potential in preventing and treating various diseases, including cancer. This study reviewed 74 literature studies published between 2006 and 2022 that conducted in vitro cytotoxicity and cell apoptosis analyses of the different concentrations of phytochemicals and their combinations with conventional drugs or supplementary phytochemicals on human pancreatic cell lines. From 34 plant-derived phytochemicals on 20 human pancreatic cancer cell lines, a total of 11 input and 2 output variables have been used to construct the data set that contained 2161 different instances. The machine learning approach has been implemented using random forest for regression, whereas association rule mining has been used to determine the effects of individual phytochemicals. The random forest models developed are generally good, indicating that the phytochemical type, its concentration, and the type of cell line are the most important descriptors for predicting the cell viability. However, for predicting cell apoptosis the primary phytochemical type is the most significant descriptor . Among the studied phytochemicals, catechin and indole-3-carbinol were found to be non-cytotoxic at all concentrations irrespective of the treatment time. On the other hand, berbamine and resveratrol were strongly cytotoxic with cell viabilities of less than 40% at a concentration range between 10 and 100 µM and above 100 µM, respectively, which brings them forward as potential therapeutic agents in the treatment of pancreatic cancer.

Coarse-grained modeling of polystyrene-modified CNTs and their interactions with lipid bilayers.

In the present work, we describe Martini3 coarse-grained models of polystyrene and carboxyl-terminated polystyrene functionalized carbon nanotubes (CNTs) and investigate their interactions with lipid bilayers with and without cholesterol (CHOL) using molecular dynamics simulations. By changing the polystyrene chain length and grafting density at the end ring of the CNTs at two different nanotube concentrations, we observe the translocation of nanoparticles as well as changes in the lipid bilayer properties. Our results show that all developed models passively diffuse into the membranes without causing any damage to the membrane integrity, although high concentrations of CNTs induce structural and elastic changes in lipid bilayers. In the presence of CHOL, increasing CNT concentration results in decreased rates of CHOL transmembrane motions. On the other hand, CNTs are prone to lipid and polystyrene blockage, which affects their equilibrated configurations, and tilting behavior within the membranes. Hence, we demonstrate that polystyrene-functionalized CNTs are promising drug-carrier agents. However, polystyrene chain length and grafting density are important factors to consider to enhance the efficiency of drug delivery.

Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery.

To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.

The Toxicity of Polystyrene-Based Nanoparticles in Saccharomyces cerevisiae Is Associated with Nanoparticle Charge and Uptake Mechanism.

Polystyrene latex (PSL) nanoparticles (NPs), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes, and hybrid NPs that have different concentrations, sizes, surface charges, and functional groups were used to determine their toxicity to Saccharomyces cerevisiae cells. The size, charge, and morphology of the nanoparticles were characterized by dynamic light scattering, electrophoretic light scattering, scanning transmission electron microscopy, and transmission electron microscopy analysis. The cell viabilities were determined by colony forming unit analysis and confocal laser scanning microscopy imaging. Uptake inhibition studies were performed to determine the internalization mechanism of PSL NPs. At 50 mg/L, both positively and negatively charged NPs were slightly toxic. With increasing concentration, however, full toxicities were observed with positively charged PSL NPs, while a marginal increase in toxicity was obtained with negatively charged PSL NPs. For negatively charged and carboxyl-functionalized NPs, an increase in size induced toxicity, whereas for positively charged and amine-functionalized NPs, smaller-sized NPs were more toxic to yeast cells. Negatively charged NPs were internalized by the yeast cells, but they showed toxicity when they entered the cell vacuole. Positively charged NPs, however, accumulated on the cell surface and caused toxicity. When coated with DOPC liposomes, positively charged NPs became significantly less toxic. We attribute this reduction to the larger-diameter and/or more-agglomerated NPs in the extracellular environment, which resulted in lower interactions with the cell. In addition to endocytosis, it is possible that the negatively charged NPs (30-C-n) were internalized by the cells, partly via direct permeation, which is preferred for high drug delivery efficiency. Negatively charged PSL NP exposure to the yeast cells at low-to-moderate concentrations resulted in low toxicities in the long term. Our results indicate that negatively charged PSL NPs provide safer alternatives as cargo carriers in drug delivery applications. Moreover, the variations in NP size, concentration, and exposure time, along with the use of hybrid systems, have significant roles in nanoparticle-based drug delivery applications in terms of their effects on living organisms.

Fullerene translocation through peroxidized lipid membranes.

Recent cytotoxicity research suggests that fullerenes can enter the cell and cross the blood-brain barrier. However, the underlying toxicity mechanism behind the penetration of fullerenes through biological membranes is still not well understood. Here we perform coarse-grained molecular dynamics simulations to investigate the interactions of fullerenes and their polar derivatives (Janus) with model regular and peroxidized bilayers. We show that the translocation of fullerenes and their residence time in bulk water vary depending on the bilayer's peroxidation degree and fullerene polarity. The distribution of fullerenes inside the bilayer is mainly determined by the peroxidation degree and the saturation level of lipid acyl chains. The transport of pristine fullerenes through bilayers occurs at nano timescale while the complete diffusion may not be achieved for Janus fullerenes in micro timescale. As for the toxic response of fullerenes in terms of membrane damage, no mechanical disruption of model bilayers is observed throughout the studied simulation times.

Understanding Interactions of Curcumin with Lipid Bilayers: A Coarse-Grained Molecular Dynamics Study.

The interactions of curcumin with various lipid bilayers (POPC, DOPC, oxidized POPC, and oxidized DOPC) and model biomembranes (symmetric bacteria and yeast plasma membranes, as well as asymmetric mammalian plasma membrane) are investigated. A nonlinear thinning effect of curcumin with respect to its concentration is demonstrated in PC membranes and in the yeast. Curcumin induces asymmetry to the symmetric yeast membranes but reduces the degree of asymmetry of the mammalian plasma membranes when the molecule is placed facing the outer leaflets. The molecule is found to diffuse through oxidized PC bilayers, POPC bilayers at a curcumin to lipid ratio C/L = 1/5, yeast membranes at C/L = 1/100, and the mammalian plasma membranes at C/L = 1/5 and when the molecule placed facing the outer leaflets. The results of this work demonstrate that the lipid type, the lipid distribution, and curcumin amount play a critical role in defining the interactions of curcumin with the lipids and their transport behavior through the bilayers.

Molecular Dynamics Modeling of Methylene Blue-DOPC Lipid Bilayer Interactions.

We present a coarse-grained MARTINI model for methylene blue (MB) and investigate the interactions of MB with dioleylphosphatidylcholine (DOPC) lipid bilayers by molecular dynamics simulations. Our results show that the charge state of MB and the oxidation degree of the DOPC bilayer play critical roles on membrane properties. Oxidation of the DOPC bilayer significantly increases permeability of water and MB molecules, irrespective of the charge state of MB. The most significant changes in membrane properties are obtained for peroxidized lipid bilayers in the presence of cationic MB, with ∼11% increase in the membrane area per lipid head group and ∼7 and 44% reduction in membrane thickness and lateral diffusivity, respectively.

Improved controlled release of protein from expanded-pore mesoporous silica nanoparticles modified with co-functionalized poly(n-isopropylacrylamide) and poly(ethylene glycol) (PNIPAM-PEG).

Novel pore-expanded mesoporous silica nanoparticles (MSNs) with pore sizes of approximately 11nm were synthesized and modified with thermoresponsive, poly(n-isopropylacrylamide) (PNIPAM) gating groups on the nanoparticle exterior surface and in addition with poly(ethylene-glycol) (PEG) within the porous interior to minimize protein adsorption. PEG traditionally has been grafted to the nanoparticle exterior to minimize non-specific binding and interactions with the biological environment, but due to the templating mechanism of MSN synthesis, both the pore interior and nanoparticle surface can be separately modified. Here, an improved control release behavior of bovine hemoglobin (BHb) was observed after PEGylating the interior porous framework, compared to the release BHb from unmodified MSNs. This can be attributed to the reduced protein denaturation on PEGylated silica that was observed using circular dichroism spectroscopy.

Understanding the Interaction of Pluronics L61 and L64 with a DOPC Lipid Bilayer: An Atomistic Molecular Dynamics Study.

We investigate the interactions of Pluronics L61 and L64 with a dioleylphosphatidylcholine (DOPC) lipid bilayer by atomistic molecular dynamics simulations using the all-atom OPLS force field. Our results show that the initial configuration of the polymer with respect to the bilayer determines its final conformation within the bilayer. When the polymer is initially placed at the lipid/water interface, we observe partial insertion of the polymer in a U-shaped conformation. On the other hand, when the polymer is centered at the bilayer, it stabilizes to a transmembrane state, which facilitates water transport across the bilayer. We show that membrane thickness decreases while its fluidity increases in the presence of Pluronics. When the polymer concentration inside the bilayer is high, pore formation is initiated with L64. Our results show good agreement with existing experimental data and reveal that the hydrophilic/lipophilic balance of the polymer plays a critical role in the interaction mechanisms as well as in the dynamics of Pluronics with and within the bilayer.