Comparative computational study of interaction of C60-fullerene and tris-malonyl-C60-fullerene isomers with lipid bilayer: relation to their antioxidant effect

Mechanism of PARP1 Elongation Reaction Revealed by Molecular Modeling

Poly(ADP-ribose) polymerase 1 (PARP1) plays a major role in the DNA damage repair and transcriptional regulation, and is targeted by a number of clinical inhibitors. Despite this, catalytic mechanism of PARP1 remains largely underexplored because of the complex substrate/product structure. Using molecular modeling and metadynamics simulations we have described in detail elongation of poly(ADP-ribose) chain in the PARP1 active site. It was shown that elongation reaction proceeds via the SN1-like mechanism involving formation of the intermediate furanosyl oxocarbenium ion. Intriguingly, nucleophilic 2'A-OH group of the acceptor substrate can be activated by the general base Glu988 not directly but through the proton relay system including the adjacent 3'A-OH group.

Self-assembly of ultra-small-sized carbon nanoparticles in lipid membrane disrupts its integrity

Although nanomaterials are widely studied in biomedical applications, the major concern of nanotoxicity still exists. Therefore, numerous studies have been conducted on the interactions of various biomolecules with various types of nanomaterials, including carbon nanotubes, graphene, fullerene etc. However, the size effect of nanomaterials is poorly documented, especially ultra-small particles. Here, the interactions of the smallest carbon nanoparticle (NP), C₂₈, with the cell membrane were studied using molecular dynamics (MD) simulations. The results show that similar to fullerene C₆₀, the C₂₈ NPs can self-assemble into stable clusters in water. Inside the membrane, the C₂₈ NPs are more prone to aggregate to form clusters than C₆₀ NPs. The reason for C₂₈ aggregation is characterized by the potential of mean force (PMF) and can be explained by the polarized nature of C₂₈ NPs while the acyl chains of lipids are nonpolar. At the C₂₈ cluster regions, the thickness of the membrane is significantly reduced by the C₂₈ aggregation. Accordingly, the membrane loses its structural integrity, and translocation of water molecules through it was observed. Thus, these results predict a stronger cytotoxicity to cells than C₆₀ NPs. The present findings might shed light on the understanding of the cytotoxicity of NPs with different sizes and would be helpful for the potential biomedical applications of carbon NPs, especially as antibacterial agents.

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C₆₀. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol⁻¹, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol⁻¹ for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C₆₀ was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C₆₀ binding.

Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study

Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.

Carbonaceous Nanomaterials-Mediated Defense Against Oxidative Stress

The concept of nanoscale materials and their applications in industrial technologies, consumer goods, as well as in novel medical therapies has rapidly escalated in the last several years. Consequently, there is a critical need to understand the mechanisms that drive nanomaterials biocompatibility or toxicity to human cells and tissues. The ability of nanomaterials to initiate cellular pathways resulting in oxidative stress has emerged as a leading hypothesis in nanotoxicology. Nevertheless, there are a few examples revealing another face of nanomaterials - they can alleviate oxidative stress via decreasing the level of reactive oxygen species. The fundamental structural and physicochemical properties of carbonaceous nanomaterials that govern these anti-oxidative effects are discussed in this article. The signaling pathways influenced by these unique nanomaterials, as well as examples of their applications in the biomedical field, e.g. cell culture, cell-based therapies or drug delivery, are presented. We anticipate this emerging knowledge of intrinsic anti-oxidative properties of carbon nanomaterials to facilitate the use of tailored nanoparticles in vivo.

The mechanisms of action of water-soluble aminohexanoic and malonic adducts of fullerene C60 with hexamethonium on model lipid membranes

In an attempt to understand the possibility of applications of the fullerene-based systems for transporting various polar compounds like hexamethonium through the blood-brain barrier, we studied the influence of a series of derivatives of fullerene C₆₀ in the form of salts with hexamethonium bis-anion, namely the adducts of fullerenols with 6-aminohexanoic acid (IEM-2197), and two bis-adduct malonic acid derivatives of fullerene with addents bound in two hemispheres (IEM-2143) and in equatorial positions (IEM-2144), on model membranes. We showed that IEM-2197 induced the disintegration of the bilayers composed of DOPC at the concentrations more than 2 mg/ml. IEM-2144 and IEM-2143-induced ion-permeable pores at concentrations of 0.3 and 0.02 mg/ml, respectively; herewith, IEM-2143 was characterized by the greater efficiency than IEM-2144. IEM-2197 did not significantly affect the phase behavior of DPPC, while the melting temperature significantly decreased with addition of IEM-2144 and IEM-2143. The increase in the half-width of the main transition peaks by more than 2.0 °C in the presence of IEM-2144 and IEM-2143 was observed, along with the pronounced peak deconvolution. We proposed that the immersion of IEM-2144 and IEM-2143 into the polar region of the DOPC or DPPC bilayers led to an increase in the relative mobility of tails and formation of ion-permeable defects. IEM-2197 demonstrated the more pronounced effects on the melting and ion permeability of PG- and PS-containing bilayers compared to PC-enriched membranes. These results indicated that IEM-2197 preferentially interacts with the negatively charged lipids compared to neutral species.

Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study

Passive permeation of CD across lipid bilayer is almost impossible. Forced permeation results membrane rupture.

C60 Fullerenes Suppress Reactive Oxygen Species Toxicity Damage in Boar Sperm

We report the carboxylated C₆₀ improved the survival and quality of boar sperm during liquid storage at 4 °C and thus propose the use of carboxylated C₆₀ as a novel antioxidant semen extender supplement. Our results demonstrated that the sperm treated with 2 μg mL^-1 carboxylated C₆₀ had higher motility than the control group (58.6% and 35.4%, respectively; P ˂ 0.05). Moreover, after incubation with carboxylated C₆₀ for 10 days, acrosome integrity and mitochondrial activity of sperm increased by 18.1% and 34%, respectively, compared with that in the control group. Similarly, the antioxidation abilities and adenosine triphosphate levels in boar sperm treated with carboxylated C₆₀ significantly increased (P ˂ 0.05) compared with those in the control group. The presence of carboxylated C₆₀ in semen extender increases sperm motility probably by suppressing reactive oxygen species (ROS) toxicity damage. Interestingly, carboxylated C₆₀ could protect boar sperm from oxidative stress and energy deficiency by inhibiting the ROS-induced protein dephosphorylation via the cAMP-PKA signaling pathway. In addition, the safety of carboxylated C₆₀ as an alternative antioxidant was also comprehensively evaluated by assessing the mean litter size and number of live offspring in the carboxylated C₆₀ treatment group. Our findings confirm carboxylated C₆₀ as a novel antioxidant agent and suggest its use as a semen extender supplement for assisted reproductive technology in domestic animals.

Enantioselective analysis of D- and l- Serine on a layer-by-layer imprinted electrochemical sensor

The present work describes a new, simple, and easy method of generating acrylamide functionalised reduced graphene oxide-fullerene layer-by-layer assembled dual imprinted polymers to quantify D- and L-Serine at ultra trace level in aqueous and real samples. Herein, the pencil graphite electrode was initially spin coated with D-Serine imprinted acrylamide functionalized reduced graphene oxide. After 10 min thermal treatment (50 °C), this electrode was again modified with L-Serine imprinted acrylamide functionalized fullerene molecules. This bilayer assembly was finally made thermally stable by 60 °C exposure for 3 h. The proposed sensor showed better electronic properties with an improved synergism. We have compared this modified electrode with other modified pencil graphite electrodes like single layered acrylamide functionalised reduced graphene oxide or fullerene, single layered acrylamide functionalised reduced graphene oxide-fullerene composite and double layered acrylamide functionalised reduced graphene oxide or fullerene molecules, which yielded very inferior sensitivity due to possible agglomeration and decreased synergism. The chosen system demonstrated a very good analytical figures of merit with differential pulse anodic stripping voltammetry and cyclic voltammetry transduction, showing lower limits of detection (0.24 ng mL^-1, S/N = 3) for both isomers. The proposed sensor assures practical applications as disease biomarker, manifesting several diseases at very ultra-trace level.

Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations

Phthalocyanines are aromatic macrocyclic compounds, which are structurally related to porphyrins. In clinical practice, phthalocyanines are used in fluorescence imaging and photodynamic therapy of cancer and noncancer lesions. Certain forms of the substituted polycationic metallophthalocyanines have been previously shown to be active in photodynamic inactivation of both Gram-negative and Gram-positive bacteria; one of them is zinc octakis(cholinyl)phthalocyanine (ZnPcChol⁸⁺). However, the molecular details of how these compounds translocate across bacterial membranes still remain unclear. In the present work, we have developed a coarse-grained (CG) molecular model of ZnPcChol⁸⁺ within the framework of the popular MARTINI CG force field. The obtained model was used to probe the solvation behavior of phthalocyanine molecules, which agreed with experimental results. Subsequently, it was used to investigate the molecular details of interactions between phthalocyanines and membranes of various compositions. The results demonstrate that ZnPcChol⁸⁺ has high affinity to both the inner and the outer model membranes of Gram-negative bacteria, although this species does not show noticeable affinity to the 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphatidylcholine membrane. Furthermore, we found out that the process of ZnPcChol⁸⁺ penetration toward the center of the outer bacterial membrane is energetically favorable and leads to its overall disturbance and formation of the aqueous pore. Such intramembrane localization of ZnPcChol⁸⁺ suggests their twofold cytotoxic effect on bacterial cells: (1) via induction of lipid peroxidation by enhanced production of reactive oxygen species (i.e., photodynamic toxicity); (2) via rendering the bacterial membrane more permeable for additional Pc molecules as well as other compounds. We also found that the kinetics of penetration depends on the presence of phospholipid defects in the lipopolysaccharide leaflet of the outer membrane and the type of counterions, which stabilize it. Thus, the results of our simulations provide a detailed molecular view of ZnPcChol⁸⁺ "self-promoted uptake", the pathway previously proposed for some small molecules crossing the outer bacterial membrane.

Quantification of C60-induced membrane disruption using a quartz crystal microbalance

Direct contact between fullerene C₆₀ nanoparticles (NPs) and cell membranes is one of mechanisms for its cytotoxicity. In this study, the influence of C₆₀ NPs on lipid membranes was investigated. Giant unilamellar vesicles (GUVs) were used as model cell membranes to observe the membrane disruption after C₆₀ exposure. C₆₀ NPs disrupted the positively charged GUVs but not the negatively charged vesicles, confirming the role of electrostatic forces. To quantify the C₆₀ adhesion on membrane and the induced membrane disruption, a supported lipid bilayer (SLB) and a layer of small unilamellar vesicles (SUVs) were used to cover the sensor of a quartz crystal microbalance (QCM). The mass change on the SLB (Δm_SLB) was caused by the C₆₀ adhesion on the membrane, while the mass change on the SUV layer (Δm_SUV) was the combined result of C₆₀ adhesion (mass increase) and SUV disruption (mass loss). The surface area of SLB (A_SLB) was much smaller than the surface area of SUV (A_SUV), but Δm_SLB was larger than Δm_SUV after C₆₀ deposition, indicating that C₆₀ NPs caused remarkable membrane disruption. Therefore a new method was built to quantify the degree of NP-induced membrane disruption using the values of Δm_SUV/Δm_SLB and A_SUV/A_SLB. In this way, C₆₀ can be compared with other types of NPs to know which one causes more serious membrane disruption. In addition, C₆₀ NPs caused negligible change in the membrane phase, indicating that membrane gelation was not the mechanism of cytotoxicity for C₆₀ NPs. This study provides important information to predict the environmental hazard presented by fullerene NPs and to evaluate the degree of membrane damage caused by different NPs.

Fullerene C₆₀ NPs adhere on lipid membrane due to electrostatic force and cause membrane disruption.

Mechanisms underlying interactions between PAMAM dendron-grafted surfaces with DPPC membranes

Biofouling is a pervasive problem which demands the creation of smart, antifouling surfaces. Towards this end, we examine the interactions between a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer and a polyamidoamine (PAMAM) dendron-grafted surface. In addition, we investigate the impact of dendron generation on the system behavior. To resolve the multiscale dynamical processes occurring over a large spatial scale, we employ Molecular Dynamics simulations with a coarse-grained implicit solvent force field. Our results demonstrate the transient and equilibrium system dynamics to be determined by the PAMAM dendron generation along with the underlying mechanisms. Higher generation dendrons are observed to favor penetration of the DPPC molecules into the dendron branches, thereby enabling sustained interactions between the membrane and the dendron-grafted surface. Under equilibrium, the membrane adopts a bowl-shaped morphology whose dimensions are determined by the dendron generation and density of interactions. The results from our study can be used to guide the design of novel surfaces with selective antifouling properties which can prevent the adsorption of microorganisms onto lipid membranes.

The interactions between a DPPC lipid membrane and a PAMAM dendron-grafted surface.

Mechanism of ROS scavenging and antioxidant signalling by redox metallic and fullerene nanomaterials: Potential implications in ROS associated degenerative disorders

BACKGROUND

The balance between oxidation and anti-oxidation is believed to be critical in maintaining healthy biological systems. However, our endogenous antioxidant defense systems are incomplete without exogenous antioxidants and, therefore, there is a continuous demand for exogenous antioxidants to prevent stress and ageing associated disorders. Nanotechnology has yielded enormous variety of nanomaterials (NMs) of which metallic and carbonic (mainly fullerenes) NMs, with redox property, have been found to be strong scavengers of ROS and antioxidants in preclinical in vitro and in vivo models.

SCOPE OF REVIEW

Redox activity of metal based NMs and membrane translocation time of fullerene NMs seem to be the major determinants in ROS scavenging potential exhibited by these NMs. A comprehensive knowledge about the effects of ROS scavenging NMs in cellular antioxidant signalling is largely lacking. This review compiles the mechanisms of ROS scavenging as well as antioxidant signalling of the aforementioned metallic and fullerene NMs.

MAJOR CONCLUSIONS

Direct interaction between NMs and proteins does greatly affect the corona/adsorption formation dynamics but such interaction does not provide the explanation behind diverse biological outcomes induced by NMs. Indirect interaction, however, that could occur via NMs uptake and dissolution, NMs ROS induction and ROS scavenging property, and NMs membrane translocation time seem to work as a central mode of interaction.

GENERAL SIGNIFICANCE

The usage of potential antioxidant NMs in biological systems would greatly impact the field of nanomedicine. ROS scavenging NMs hold great promise in the future treatment of ROS related degenerative disorders.

Biological potential of nanomaterials strongly depends on the suspension media: experimental data on the effects of fullerene C₆₀ on membranes

Fullerenes (C60) are some of the most promising carbon nanomaterials to be used for medical applications as drug delivery agents. Computational and experimental studies have proposed their ability to enter cells by penetrating lipid bilayers. The aim of our study was to provide experimental evidence on whether pristine C60 in physiological media could penetrate cell membranes. The effect was tested on phospholipid vesicles (liposomes) composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, and validated on isolated human red blood cells (RBCs). We incubated the liposomes in an aqueous suspension of C60 and dissolved the lipids and C60 together in chloroform and subsequently formatted the liposomes. By differential scanning calorimetry measurements, we assessed the effect of C60 on the phospholipid thermal profile. The latter was not affected after the incubation of liposomes in the C60 suspension; also, a shape transformation of RBCs did not occur. Differently, by dispersing both C60 and the phospholipids in chloroform, we confirmed the possible interaction of C60 with the bilayer. We provide experimental data suggesting that the suspension medium is an important factor in determining the C60-membrane interaction, which is not always included in computational studies. Since the primary particle size is not the only crucial parameter in C60-membrane interactions, it is important to determine the most relevant characteristics of their effects on membranes.

Blocking the passage: C60 geometrically clogs K(+) channels

Classical molecular dynamics (MD) simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and molecular mechanic/Poisson-Boltzmann surface area (MM-PBSA) energy calculations reveal that C60 may block K(+) channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ∼21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in solvent accessible surface area upon C60 binding shows that binding at this site is governed purely by shape complementarity, and that the molecular determinants of binding are conserved in the entire family of K(+) channels. The presence of this high-affinity binding site conserved among different K(+) channels may have serious implications for the toxicity of carbon nanomaterials.