Controlled and Selective Photo-oxidation of Amyloid-ß Fibrils by Oligomeric p-Phenylene Ethynylenes.

Photodynamic therapy (PDT) has been explored as a therapeutic strategy to clear toxic amyloid aggregates involved in neurodegenerative disorders such as Alzheimer's disease. A major limitation of PDT is off-target oxidation, which can be lethal for the surrounding cells. We have shown that a novel class of oligo-p-phenylene ethynylenes (OPEs) exhibit selective binding and fluorescence turn-on in the presence of prefibrillar and fibrillar aggregates of disease-relevant proteins such as amyloid-ß (Aß) and α-synuclein. Concomitant with fluorescence turn-on, OPE also photosensitizes singlet oxygen under illumination through the generation of a triplet state, pointing to the potential application of OPEs as photosensitizers in PDT. Herein, we investigated the photosensitizing activity of an anionic OPE for the photo-oxidation of Aß fibrils and compared its efficacy to the well-known but nonselective photosensitizer methylene blue (MB). Our results show that, while MB photo-oxidized both monomeric and fibrillar conformers of Aß40, OPE oxidized only Aß40 fibrils, targeting two histidine residues on the fibril surface and a methionine residue located in the fibril core. Oxidized fibrils were shorter and more dispersed but retained the characteristic ß-sheet rich fibrillar structure and the ability to seed further fibril growth. Importantly, the oxidized fibrils displayed low toxicity. We have thus discovered a class of novel theranostics for the simultaneous detection and oxidization of amyloid aggregates. Importantly, the selectivity of OPE's photosensitizing activity overcomes the limitation of off-target oxidation of traditional photosensitizers and represents an advancement of PDT as a viable strategy to treat neurodegenerative disorders.

Computational Investigation of the Binding Dynamics of Oligo p-Phenylene Ethynylene Fluorescence Sensors and Aß Oligomers.

Amyloid protein aggregates are pathological hallmarks of neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's (PD) diseases and are believed to be formed well before the onset of neurodegeneration and cognitive impairment. Monitoring the course of protein aggregation is thus vital to understanding and combating these diseases. We have recently demonstrated that a novel class of fluorescence sensors, oligomeric p-phenylene ethynylene (PE)-based electrolytes (OPEs) selectively bind to and detect prefibrillar and fibrillar aggregates of AD-related amyloid-ß (Aß) peptides over monomeric Aß. In this study, we investigated the binding between two OPEs, anionic OPE12- and cationic OPE24+, and to two different ß-sheet rich Aß oligomers using classical all-atom molecular dynamics simulations. Our simulations have revealed a number of OPE binding sites on Aß oligomer surfaces, and these sites feature hydrophobic amino acids as well as oppositely charged amino acids. Binding energy calculations show energetically favorable interactions between both anionic and cationic OPEs with Aß oligomers. Moreover, OPEs bind as complexes as well as single molecules. Compared to free OPEs, Aß protofibril bound OPEs show backbone planarization with restricted rotations and reduced hydration of the ethyl ester end groups. These characteristics, along with OPE complexation, align with known mechanisms of binding induced OPE fluorescence turn-on and spectral shifts from a quenched, unbound state in aqueous solutions. This study thus sheds light on the molecular-level details of OPE-Aß protofibril interactions and provides a structural basis for fluorescence turn-on sensing modes of OPEs.

Computational Study of the Driving Forces and Dynamics of Curcumin Binding to Amyloid-ß Protofibrils.

Oligomeric aggregates of the amyloid-ß (Aß) peptide are believed to be the primary toxic species that initiate events leading to neurodegeneration and cognitive decline in Alzheimer's disease (AD). Small molecules that interfere with Aß aggregation and/or neurotoxicity are being investigated as potential therapeutics for AD, including naturally occurring polyphenols. We have recently shown that curcumin exerts a neuroprotective effect against Aß40-induced toxicity on cultured neuronal cells through two possible concerted pathways, ameliorating Aß oligomer-induced toxicity and inducing the formation of nontoxic Aß oligomers, both of which involve curcumin binding to Aß oligomers. To gain molecular-level insights into curcumin's interaction with Aß oligomers, we use all-atom molecular dynamics (MD) simulations to study the dynamics and energetics of curcumin binding to an Aß protofibril composed of 24 peptides. Our results show that curcumin binds to specific hydrophobic sites on the protofibril surface and that binding is generally associated with the concomitant complexation of curcumin into dimers, trimers, or tetramers. Curcumin also binds to the protofibril growth axis ends but without complexation. Analysis of the energetics of the binding process revealed that curcumin complexation contributes in an additive fashion to curcumin-Aß protofibril interactions. Favorable curcumin-protofibril binding is driven by a combination of hydrophobic interactions between curcumin and protofibril, curcumin self-aggregation, and solvation effects. These interactions are likely critical in blocking Aß oligomer toxicity and inducing the growth of the protofibrils into "off-pathway" wormlike fibrils observed experimentally.

Oligomeric Conjugated Polyelectrolytes Display Site-Preferential Binding to an MS2 Viral Capsid.

Opportunistic bacteria and viruses are a worldwide health threat prompting the need to develop new targeting modalities. A class of novel synthetic poly(phenylene ethynylene) (PPE)-based oligomeric conjugated polyelectrolytes (OPEs) have demonstrated potent wide-spectrum biocidal activity. A subset of cationic OPEs display high antiviral activity against the MS2 bacteriophage. The oligomers have been found to inactivate the bacteriophage and perturb the morphology of the MS2 viral capsid. However, details of the initial binding and interactions between the OPEs and the viruses are not well understood. In this study, we use a multiscale computational approach, including random sampling, molecular dynamics, and electronic structure calculations, to gain an understanding of the molecular-level interactions of a series of OPEs that vary in length, charge, and functional groups with the MS2 capsid. Our results show that OPEs strongly bind to the MS2 capsid protein assembly with binding energies of up to -30 kcal/mol. Free-energy analysis shows that the binding is dominated by strong van der Waals interactions between the hydrophobic OPE backbone and the capsid surface and strong electrostatic free energy contributions between the OPE charged moieties and charged residues on the capsid surface. This knowledge provides molecular-level insight into how to tailor the OPEs to optimize viral capsid disruption and increase OPE efficacy to target amphiphilic protein coats of icosahedral-based viruses.

Diblock copolymer micelles and supported films with noncovalently incorporated chromophores: a modular platform for efficient energy transfer.

We report generation of modular, artificial light-harvesting assemblies where an amphiphilic diblock copolymer, poly(ethylene oxide)-block-poly(butadiene), serves as the framework for noncovalent organization of BODIPY-based energy donor and bacteriochlorin-based energy acceptor chromophores. The assemblies are adaptive and form well-defined micelles in aqueous solution and high-quality monolayer and bilayer films on solid supports, with the latter showing greater than 90% energy transfer efficiency. This study lays the groundwork for further development of modular, polymer-based materials for light harvesting and other photonic applications.

Enzyme-specific sensors via aggregation of charged p-phenylene ethynylenes.

Chemical and biological sensors are sought for their ability to detect enzymes as biomarkers for symptoms of various disorders, or the presence of chemical pollutants or poisons. p-Phenylene ethynylene oligomers with pendant charged groups have been recently shown to have ideal photophysical properties for sensing. In this study, one anionic and one cationic oligomer are combined with substrates that are susceptible to enzymatic degradation by phospholipases or acetylcholinesterases. The photophysical properties of the J-aggregated oligomers with the substrate are ideal for sensing, with fluorescence quantum yields of the sensors enhanced between 30 and 66 times compared to the oligomers without substrate. The phospholipase sensor was used to monitor the activity of phospholipase A1 and A2 and obtain kinetic information, though phospholipase C did not degrade the sensor. The acetylcholinesterase sensor was used to monitor enzyme activity and was also used to detect the inhibition of acetylcholinesterase by three different inhibitors. Phospholipase A2 is a biomarker for heart and circulatory disease, and acetylcholinesterase is a biomarker for Alzheimer's, and indicative of exposure to certain pesticides and nerve agents. This work shows that phenylene ethynylene oligomers can be tailored to enzyme-specific sensors by careful selection of substrates that induce formation of a molecular aggregate, and that the sensing of enzymes can be extended to enzyme kinetics and detection of inhibition. Furthermore, the aggregates were studied through all-atom molecular dynamics, providing a molecular-level view of the formation of the molecular aggregates and their structure.

Computational study of bacterial membrane disruption by cationic biocides: structural basis for water pore formation.

The development of biocides as disinfectants that do not induce bacterial resistance is crucial to health care since hospital-acquired infections afflict millions of patients every year. Recent experimental studies of a class of cationic biocides based on the phenylene ethynylene backbone, known as OPEs, have revealed that their biocidal activity is accompanied by strong morphology changes to bacterial cell membranes. In vitro studies of bacterial membrane mimics have shown changes to the lipid phase that are dependent on the length and orientation of the cationic moieties on the backbone. This study uses classical molecular dynamics to conduct a comprehensive survey of how oligomers with different chemical structures interact with each other and with a bacterial cell membrane mimic. In particular, the ability of OPEs to disrupt membrane structure is studied as a function of the length of the biocides and the orientation of their cationic moieties along the backbone of the molecule. The simulation results show that the structure of OPEs radically affects their interactions with a lipid bilayer. Biocides with branched cationic groups form trans-membrane water pores regardless of their backbone length, while only 1-1.5 nm of membrane thinning is observed with biocides with cationic groups on their terminal ends. The molecular dynamics simulations provide mechanistic details at the molecular level of the interaction of these biocidal oligomers and the lipid bilayer and corroborate experimental findings regarding observed differences in membrane disruption by OPEs with different chemical structures.

Calculation of iron transport through human H-chain ferritin.

Influx of ferrous ions from the cytoplasm through 3-fold pores in the shell of ferritin protein is computed using a 3-dimensional Poisson-Nernst-Planck electrodiffusion model, with inputs such as the pore structure and the diffusivity profile of permeant Fe(2+) ions extracted from all-atom molecular dynamics (MD) simulations. These calculations successfully reproduce experimental estimates of the transit time of Fe(2+) through the ferritin coat, which is on the millisecond time scale and hence much too long to be directly simulated via all-atom MD. This is also much longer than the typical time scale for ion transit in standard membrane spanning ion channels whose pores bear structural similarity to that of the 3-fold ferritin pore. The slow time scale for Fe(2+) transport through ferritin pores is traced to two features that distinguish the ferritin pore system from standard ion channels, namely, (i) very low concentration of cytoplasmic Fe(2+) under physiological conditions and (ii) very small internal diffusion coefficients for ions inside the ferritin pore resulting from factors that include the divalent nature of Fe(2+) and two rings of negatively charged amino acids surrounding a narrow geometric obstruction within the ferritin pore interior.

Cationic oligo-p-phenylene ethynylenes form complexes with surfactants for long-term light-activated biocidal applications.

Cationic oligo-p-phenylene ethynylenes are highly effective light-activated biocides that deal broad-spectrum damage to a variety of pathogens, including bacteria. A potential problem arising in the long-term usage of these compounds is photochemical breakdown, which nullifies their biocidal activity. Recent work has shown that these molecules complex with oppositely-charged surfactants, and that the resulting complexes are protected from photodegradation. In this manuscript, we determine the biocidal activity of an oligomer and a complex formed between it and sodium dodecyl sulfate. The complexes are able to withstand prolonged periods of irradiation, continuing to effectively kill both Gram-negative and Gram-positive bacteria, while the oligomer by itself loses its biocidal effectiveness quickly in the presence of light. In addition, damage and stress responses induced by these biocides in both E. coli and S. aureus are discussed. This work shows that complexation with surfactants is a viable method for long-term light-activated biocidal applications.

Structural basis for aggregation mode of oligo-p-phenylene ethynylenes with ionic surfactants.

In this letter, the aggregation modes of two classes of ionic p-phenylene ethynylene oligomers with oppositely charged surfactants are studied. The location of the ionic side chains was found to influence the type of aggregate formed when an equivalent number of surfactant molecules are added to solution. When the charged groups were located at the terminal ends of the molecule, strong H-aggregates were observed to form. Alternatively, when the ionic groups were both located on opposite sides of the central phenyl ring, the formation of J-aggregates was observed. Interestingly, as the surfactant concentration approaches the critical micelle concentration, the weakly bound aggregates are dissociated and the absorbance spectrum returns to what is observed in water. This study reveals the structural basis for aggregation effects between molecules based on the p-phenylene ethynylene backbone, and gives an understanding of how to influence the aggregation mode of similar compounds.

Photochemistry of "end-only" oligo-p-phenylene ethynylenes: complexation with sodium dodecyl sulfate reduces solvent accessibility.

Cationic oligo-p-phenylene ethynylenes are very effective light-activated biocides and biosensors but degrade upon exposure to light. In this study, we explore the photochemistry of a class of "end-only" compounds from this series, which have cationic moieties on the ends of the backbone. Product characterization by mass spectrometry reveals that the photoreactivity of these molecules is higher than that of a previously studied oligomer and that the primary products of photolysis result from the addition of water or oxygen across the triple bond. In addition, a product suggesting the addition of peroxide or other reactive oxygen species across the triple bond was observed. To explore avenues by which the photodegradation of these compounds can be mitigated, the effects of complexation with sodium dodecyl sulfate micelles on their photochemistry was explored. Classical molecular dynamics simulations revealed that compounds that were protected from photolysis by SDS buried their phenylene ethynylene backbones into the interior of the micelle, protecting it from contact with water. This work has revealed a molecular basis for the protection of a novel class of light-activated biocides from irradiation that is consistent with the proposed photochemistry of these compounds. This information can be useful for developing photodegradation-resistant biocidal materials and applications for current compounds and leads to new molecular design.

Metal binding sites of human H-chain ferritin and iron transport mechanism to the ferroxidase sites: a molecular dynamics simulation study.

We study via all atom classical molecular dynamics (MD) simulation the process of uptake of ferrous ions (Fe(2+)) into the human ferritin protein and the catalytic ferroxidase sites via pores ("channels") in the interior of the protein. We observe that the three-fold hydrophilic channels serve as the main entrance pathway for the Fe(2+) ions. The binding sites along the ion pathway are investigated. Two strong binding sites, at the Asp131 and Glu134 residues and two weak binding sites, at the His118 and Cys130 are observed inside the three-fold channel. We also identify an explicit pathway for an ion exiting the channel into the central core of the protein as it moves to the ferroxidase site. The diffusion of an Fe(2+) ion from the inner opening of the channel to a ferroxidase site located in the interior region of the protein coat is assisted by Thr135, His136 and Tyr137. The Fe(2+) ion binds preferentially to site A of the ferroxidase site.

Molecular dynamics simulation study of the interaction of cationic biocides with lipid bilayers: aggregation effects and bilayer damage.

A novel class of phenylene ethynylene polyelectrolyte oligomers (OPEs) has been found to be effective biocidal agents against a variety of pathogens. The mechanism of attack is not yet fully understood. Recent studies have shown that OPEs cause catastrophic damage to large unilamellar vesicles. This study uses classical molecular dynamics (MD) simulations to understand how OPEs interact with model lipid bilayers. All-atom molecular dynamics simulations show that aggregates of OPEs inserted into the membrane cause significant structural damage and create a channel, or pore, that allows significant leakage of water through the membrane on the 0.1 µs time scale.

A molecular dynamics and computational study of ligand docking and electron transfer in ferritins.

The mechanism of the reductive release of iron from the cavity of the iron storage protein, ferritin, has been difficult to confirm on the molecular level using experimental studies. In this paper, we use a variety of computational tools to study the binding of flavin redox agents to the protein surface, and the subsequent electron transfer (ET) through the protein coat. Flavin binding sites are identified that represent efficient routes to reduction of Fe(III) across the protein coat in human and bacterial ferritins. Using the pathways model and Dutton's packing density model, we show that ET across the protein coat to nucleation sites is feasible. Different protein configurations for human heavy and light chain ferritin were obtained along classical molecular dynamics trajectories and used for flavin binding and ET studies. We find that protein configuration affects both the binding and ET rate constants significantly. We show that the maximum possible ET rate constants to the nucleation site GLU-61 in human heavy chain ferritin for protein configurations along a MD simulation trajectory can differ by about 8 orders of magnitude compared to the crystal structure and in human light-chain ferritin rate constants vary by about 4 orders of magnitude.

Photochemistry of a Model Cationic p-Phenylene Ethynylene in Water.

One important aspect of p-phenylene-ethynylenes that has not yet been explored is the possible photochemical reactions that can take place in different chemical environments. This is especially important when considering the possible breakdown of these compounds in applications that involve exposure to light, air, and water. In this Letter, a study of the photochemical reaction processes of a cationic oligomer based on the p-phenylene-ethynylene repeat unit is performed in aqueous solution in both the presence and absence of oxygen. Clearly different reaction pathways were observed in the presence and absence of oxygen in aqueous solution. The results of this study revealed the photoaddition of water across the triple bond of the ethynyl group in the absence of oxygen, the addition of singlet-oxygen across the triple-bond in the presence of oxygen, and the cleavage of the alkoxy side chains leaving phenols in both cases.

The targeted delivery of multicomponent cargos to cancer cells by nanoporous particle-supported lipid bilayers.

Encapsulation of drugs within nanocarriers that selectively target malignant cells promises to mitigate side effects of conventional chemotherapy and to enable delivery of the unique drug combinations needed for personalized medicine. To realize this potential, however, targeted nanocarriers must simultaneously overcome multiple challenges, including specificity, stability and a high capacity for disparate cargos. Here we report porous nanoparticle-supported lipid bilayers (protocells) that synergistically combine properties of liposomes and nanoporous particles. Protocells modified with a targeting peptide that binds to human hepatocellular carcinoma exhibit a 10,000-fold greater affinity for human hepatocellular carcinoma than for hepatocytes, endothelial cells or immune cells. Furthermore, protocells can be loaded with combinations of therapeutic (drugs, small interfering RNA and toxins) and diagnostic (quantum dots) agents and modified to promote endosomal escape and nuclear accumulation of selected cargos. The enormous capacity of the high-surface-area nanoporous core combined with the enhanced targeting efficacy enabled by the fluid supported lipid bilayer enable a single protocell loaded with a drug cocktail to kill a drug-resistant human hepatocellular carcinoma cell, representing a 10(6)-fold improvement over comparable liposomes.

Synthesis, self-assembly, and photophysical properties of cationic oligo(p-phenyleneethynylene)s.

Three series of cationic oligo p-phenyleneethynylenes (OPEs) have been synthesized to study their structure-property relationships and gain insights into the transition from molecular to macromolecular properties. The absorbance maxima and molar extinction coefficients in all three sets increase with increasing number of repeat units; however, the increase in λ(max) between the oligomers having 2 and 3 repeat units is very small, and the oligomer having 3 repeat units shows virtually the same spectra as a p-phenyleneethynylene polymer having 49 repeat units. A computational study of the oligomers using density functional theory calculations indicates that while the simplest oligomers (OPE-1) are fully conjugated, the larger oligomers are nonplanar and the limiting "segment chromophore" may be confined to a near-planar segment extending over three or four phenyl rings. Several of the OPEs self-assemble on anionic "scaffolds", with pronounced changes in absorption and fluorescence. Both experimental and computational results suggest that the planarization of discrete conjugated segments along the phenylene-ethynylene backbone is predominantly responsible for the photophysical characteristics of the assemblies formed from the larger oligomers. The striking differences in fluorescence between methanol and water are attributed to reversible nucleophilic attack of structured interfacial water on the excited singlet state.

Effectiveness of perturbation theory approaches for computing non-condon electron transfer dynamics in condensed phases.

A description of electron transfer in condensed-phase media requires models that adequately describe the coupling of the electronic degrees of freedom to the surrounding nuclear coordinates. The spin-boson model has been the canonical model used to understand quantum dynamic processes in condensed-phase media over the last 25 years. Inherent in the standard model of a two-state quantum system coupled to a bosonic bath is the assumption that the Condon approximation is valid. In this context, the Condon approximation assumes that the bath configurations (coordinates) have no effect on the nonadiabatic coupling matrix element. While this is a useful model for electron transfer in small molecular systems, the validity of this approximation is less likely when large-scale motions of solvent molecules are strongly coupled to the electron transfer event, e.g., in molecular clamps and long-range electron transfer in biopolymers. In the present paper a general model for two-state electron transfer which allows for system-bath coupling in both the diagonal and off-diagonal (nonadiabatic) terms is studied. Time-dependent perturbation theory for this Hamiltonian is developed using a small polaron transformation. As noted in several recent studies, in a certain regime of parameter space, the relevant Hamiltonian admits an exact solution, termed the exactly solvable non-Condon Hamiltonian (or NCE). This limit, for which exact solutions are available, is used to benchmark the short- and long-time accuracy of various perturbative approaches. The validated perturbation equations are subsequently used to explore the role of non-Condon effects on electron transfer by systematically increasing the strength of the non-Condon coupling term from zero (i.e., the canonical spin-boson model) to the value that pertains to the exactly solvable non-Condon model (where non-Condon effects are significant).

Condensed-phase relaxation of multilevel quantum systems. I. An exactly solvable model.

An analytically solvable model of multilevel condensed-phase quantum dynamics relevant to vibrational relaxation and electron transfer is presented. Exact solutions are derived for the reduced system density matrix dynamics of a degenerate N-level quantum system characterized by nearest-neighbor hopping and off-diagonal coupling (which is linear in the bath coordinates) to a harmonic oscillator bath. We demonstrate that for N> 2 the long-time steady-state system site occupation probabilities are not the same for all sites; that is, they are distributed in a non-Boltzmann manner, which depends on the initial conditions and the number of levels in the system. Although the system-bath Hamiltonian considered here is restricted in form, the availability of an exact solution enables us to study the model in all regions of an extensive parameter space.

Condensed-phase relaxation of multilevel quantum systems. II. Comparison of path integral calculations and second-order relaxation theory for a nondegenerate three-level system.

An exactly solvable model of multisite condensed-phase vibrational relaxation was studied in Paper I (Peter, S.; Evans, D. G.; Coalson, R. D. J. Phys. Chem. B 2006, 110, 18758.), where it was shown that long-time steady-state site populations of a degenerate N-level system are not equal (hence, they are non-Boltzmann) and depend on the initial preparation of the system and the number of sites that it comprises. Here we consider a generalization of the model to the case of a nondegenerate three-level system coupled to a high-dimensional bath: such a model system has direct relevance to a large class of donor-bridge-acceptor electron transfer processes. Because the quantum dynamics of this system cannot be computed analytically, we compare numerically exact path integral calculations to the predictions of second-order time-local relaxation theory. For modest system-bath coupling strengths, the two sets of results are in excellent agreement. They show that non-Boltzmann long-time steady-state site populations are obtained when the level splitting is small but nonzero, whereas at larger values of the system bias (asymmetry) these populations become Boltzmann distributed.