Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVß3.

Inhibitors of integrin αVß3 have therapeutic promise for a variety of diseases. Most αVß3-targeting small molecules patterned after the RGD motif are partial agonists because they induce a high-affinity, ligand-binding conformation and prime the receptor to bind the ligand without an activating stimulus, in part via a charge-charge interaction between their aspartic acid carboxyl group and the metal ion in the metal-ion-dependent adhesion site (MIDAS). Building upon our previous studies on the related integrin αIIbß3, we searched for pure αVß3 antagonists that lack this typical aspartic acid carboxyl group and instead engage through direct binding to one of the coordinating residues of the MIDAS metal ion, specifically ß3 E220. By in silico screening of two large chemical libraries for compounds interacting with ß3 E220, we indeed discovered a novel molecule that does not contain an acidic carboxyl group and does not induce the high-affinity, ligand-binding state of the receptor. Functional and structural characterization of a chemically optimized version of this compound led to the discovery of a novel small-molecule pure αVß3 antagonist that (i) does not prime the receptor to bind the ligand and does not induce hybrid domain swing-out or receptor extension as judged by antibody binding and negative-stain electron microscopy, (ii) binds at the RGD-binding site as predicted by metadynamics rescoring of induced-fit docking poses and confirmed by a cryo-electron microscopy structure of the compound-bound integrin, and (iii) coordinates the MIDAS metal ion via a quinoline moiety instead of an acidic carboxyl group.

Amphiphilic Distyrylbenzene Derivatives as Potential Therapeutic and Imaging Agents for Soluble and Insoluble Amyloid ß Aggregates in Alzheimer's Disease.

Alzheimer's Disease (AD) is the most common neurodegenerative disease, and efficient therapeutic and early diagnostic agents for AD are still lacking. Herein, we report the development of a novel amphiphilic compound, LS-4, generated by linking a hydrophobic amyloid-binding distyrylbenzene fragment with a hydrophilic triazamacrocycle, which dramatically increases the binding affinity toward various amyloid ß (Aß) peptide aggregates, especially for soluble Aß oligomers. Moreover, upon the administration of LS-4 to 5xFAD mice, fluorescence imaging of LS-4-treated brain sections reveals that LS-4 can penetrate the blood-brain barrier and bind to the Aß oligomers in vivo. In addition, the treatment of 5xFAD mice with LS-4 reduces the amount of both amyloid plaques and associated phosphorylated tau aggregates vs the vehicle-treated 5xFAD mice, while microglia activation is also reduced. Molecular dynamics simulations corroborate the observation that introducing a hydrophilic moiety into the molecular structure of LS-4 can enhance the electrostatic interactions with the polar residues of the Aß species. Finally, exploiting the Cu2+-chelating property of the triazamacrocycle, we performed a series of imaging and biodistribution studies that show the 64Cu-LS-4 complex binds to the amyloid plaques and can accumulate to a significantly larger extent in the 5xFAD mouse brains vs the wild-type controls. Overall, these results illustrate that the novel strategy, to employ an amphiphilic molecule containing a hydrophilic moiety attached to a hydrophobic amyloid-binding fragment, can increase the binding affinity for both soluble and insoluble Aß aggregates and can thus be used to detect and regulate various Aß species in AD.

Broad-spectrum non-toxic antiviral nanoparticles with a virucidal inhibition mechanism.

Viral infections kill millions yearly. Available antiviral drugs are virus-specific and active against a limited panel of human pathogens. There are broad-spectrum substances that prevent the first step of virus-cell interaction by mimicking heparan sulfate proteoglycans (HSPG), the highly conserved target of viral attachment ligands (VALs). The reversible binding mechanism prevents their use as a drug, because, upon dilution, the inhibition is lost. Known VALs are made of closely packed repeating units, but the aforementioned substances are able to bind only a few of them. We designed antiviral nanoparticles with long and flexible linkers mimicking HSPG, allowing for effective viral association with a binding that we simulate to be strong and multivalent to the VAL repeating units, generating forces (∼190 pN) that eventually lead to irreversible viral deformation. Virucidal assays, electron microscopy images, and molecular dynamics simulations support the proposed mechanism.  These particles show no cytotoxicity, and in vitro nanomolar irreversible activity against herpes simplex virus (HSV), human papilloma virus, respiratory syncytial virus (RSV), dengue and lenti virus. They are active ex vivo in human cervicovaginal histocultures infected by HSV-2 and in vivo in mice infected with RSV.

Computational studies of micellar and nanoparticle nanomedicines.

Nanomedicines are typically formed by nanocarriers which can deliver in a targeted manner drugs poorly soluble in blood, increase their therapeutic activities, and reduce their side effects. Many tested nanomedicines are formed by lipids, polymers, and other amphiphilic molecules isolated or self-assembled into various complexes and micelles, functionalized nanoparticles, and other bio-compatible composite materials. Here, we show how atomistic molecular dynamics simulations can be used to characterize and optimize the structure, stability, and activity of selected nanomedicines. We discuss modeling of nanomedicines based on micelles, which can deliver selected therapeutic agents, and nanoparticles designed to act like large drugs. We show how to model nanomedicines interacting with lipid membranes, viruses, and amyloid fibrils.

Transient Clustering of Reaction Intermediates during Wet Etching of Silicon Nanostructures.

Wet chemical etching is a key process in fabricating silicon (Si) nanostructures. Currently, wet etching of Si is proposed to occur through the reaction of surface Si atoms with etchant molecules, forming etch intermediates that dissolve directly into the bulk etchant solution. Here, using in situ transmission electron microscopy (TEM), we follow the nanoscale wet etch dynamics of amorphous Si (a-Si) nanopillars in real-time and show that intermediates generated during alkaline wet etching first aggregate as nanoclusters on the Si surface and then detach from the surface before dissolving in the etchant solution. Molecular dynamics simulations reveal that the molecules of etch intermediates remain weakly bound to the hydroxylated Si surface during the etching and aggregate into nanoclusters via surface diffusion instead of directly diffusing into the etchant solution. We confirmed this model experimentally by suppressing the formation of nanoclusters of etch intermediates on the Si surfaces by shielding the hydroxylated Si sites with large ions. These results suggest that the interaction of etch intermediates with etching surfaces controls the solubility of reaction intermediates and is an important parameter in fabricating densely packed clean 3D nanostructures for future generation microelectronics.

Template-Free Hierarchical Self-Assembly of Iron Diselenide Nanoparticles into Mesoscale Hedgehogs.

The ability of semiconductor nanoparticles (NPs) to self-assemble has been known for several decades. However, the limits of the geometrical and functional complexity for the self-assembled nanostructures made from simple often polydispersed NPs are still continuing to amaze researchers. We report here the self-assembly of primary ∼2-4 nm FeSe2 NPs with puck-like shapes into either (a) monocrystalline nanosheets ∼5.5 nm thick and ∼1000 nm in lateral dimensions or (b) mesoscale hedgehogs ∼550 nm in diameter with spikes of ∼250 nm in length, and ∼10-15 nm in diameter, the path of the assembly is determined by the concentration of dodecanethiol (DT) in the reaction media. The nanosheets represent the constitutive part of hedgehogs. They are rolled into scrolls and assembled around a single core with distinct radial orientation forming nanoscale "needles" approximately doubling its fractal dimension of these objects. The core is assembled from primary NPs and nanoribbons. The size distribution of the mesoscale hedgehogs can be as low as 3.8%, indicating a self-limited mechanism of the assembly. Molecular dynamics simulation indicates that the primary FeSe2 particles have mobile edge atoms and asymmetric basal surfaces. The top-bottom asymmetry of the puck-like NPs originates from the Fe-rich/Se-rich stripes on the (011) surface of the orthorhombic FeSe2 crystal lattice, displaying 2.7 nm periodicity that is comparable to the lateral size of the primary NPs. As the concentration of DT increases, the NPs bind to additional metal sites, which increases the chemical and topographic asymmetry and switches the assembly pathways from nanosheets to hedgehogs. These results demonstrate that the self-assembly of NPs with non-biological surface ligands and without any biological templates results in morphogenesis of inorganic superstructures with complexity comparable to that of biological assemblies, for instance mimivirus. The semiconductor nature of FeSe2 hedgehogs enables their utilizations in catalysis, drug delivery, optics, and energy storage.

Highly Sensitive Capacitive Gas Sensing at Ionic Liquid-Electrode Interfaces.

We have developed an ultrasensitive gas-detection method based on the measurement of a differential capacitance of electrified ionic liquid (IL) electrode interfaces in the presence and absence of adsorbed gas molecules. The observed change of differential capacitance has a local maximum at a certain potential that is unique for each type of gas, and its amplitude is related to the concentration of the gas molecules. We establish and validate this gas-sensing method by characterizing SO2 detection at ppb levels with less than 1.8% signal from other interfering species (i.e., CO2, O2, NO2, NO, SO2, H2O, H2, and cyclohexane, tested at the same concentration as SO2). This study opens a new avenue of utilizing tunable electrified IL-electrode interfaces for selective sensing of molecules with a kinetic size resolution of 0.1 Å.

Star-shaped tetraspermine enhances cellular uptake and cytotoxicity of T-oligo in prostate cancer cells.

PURPOSE: An oligonucleotide termed 'T-oligo' having sequence homology with telomere overhang has shown cytotoxicity in multiple cancers. We have demonstrated that T-oligo can induce apoptosis in androgen independent prostate cancer cell line DU-145. In this report, we evaluate the use of star-shaped tetraspermine (SSTS) for delivery of T-oligo. METHODS: SSTS was synthesized from spermine and its intrinsic cytotoxicity towards DU-145 cells was compared with spermine and branched polyethyleneimine (bPEI). Atomistic molecular dynamic (MD) simulations were conducted to understand binding and complexation of spermine and SSTS with T-oligo. Complexation was also determined using gel electrophoresis and SYBR gold assay. Complexes were characterized for size, cellular uptake and antiproliferative effect. RESULTS: SSTS exhibited significantly lower toxicity than spermine and bPEI. Its affinity towards T-oligo was significantly higher than spermine as determined by experimental studies and confirmed by MD simulations and it formed stable complexes (TONPs) with T-oligo. TONPs facilitated cellular uptake and nuclear accumulation of T-oligo and their cytotoxic potential was observed at concentration several folds lower than that required for T-oligo alone. CONCLUSION: SSTS significantly enhanced therapeutic benefits associated with the use of T-oligo and can be developed as a delivery vehicle for its in-vivo therapeutic applications.

Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue.

The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural characterization of LBD Asyn fibrils and approaches for studying disease mechanisms, imaging agents and therapeutics targeting Asyn.

Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue.

The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-21 helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.

Carbon dioxide transport across membranes.

Carbon dioxide (CO2) movement across cellular membranes is passive and governed by Fick's law of diffusion. Until recently, we believed that gases cross biological membranes exclusively by dissolving in and then diffusing through membrane lipid. However, the observation that some membranes are CO2 impermeable led to the discovery of a gas molecule moving through a channel; namely, CO2 diffusion through aquaporin-1 (AQP1). Later work demonstrated CO2 diffusion through rhesus (Rh) proteins and NH3 diffusion through both AQPs and Rh proteins. The tetrameric AQPs exhibit differential selectivity for CO2 versus NH3 versus H2O, reflecting physico-chemical differences among the small molecules as well as among the hydrophilic monomeric pores and hydrophobic central pores of various AQPs. Preliminary work suggests that NH3 moves through the monomeric pores of AQP1, whereas CO2 moves through both monomeric and central pores. Initial work on AQP5 indicates that it is possible to create a metal-binding site on the central pore's extracellular face, thereby blocking CO2 movement. The trimeric Rh proteins have monomers with hydrophilic pores surrounding a hydrophobic central pore. Preliminary work on the bacterial Rh homologue AmtB suggests that gas can diffuse through the central pore and three sets of interfacial clefts between monomers. Finally, initial work indicates that CO2 diffuses through the electrogenic Na/HCO3 cotransporter NBCe1. At least in some cells, CO2-permeable proteins could provide important pathways for transmembrane CO2 movements. Such pathways could be amenable to cellular regulation and could become valuable drug targets.

Computational screening of nanoparticles coupling to Aß40 peptides and fibrils.

Blocking the formation, growth, and breaking of amyloid fibrils by synthetic nanosystems could provide a treatment of neurodegenerative diseases. With this in mind, here atomistic molecular dynamics simulations are used to screen for nanoparticles (NPs), covered with different mixtures of ligands, including positively and negatively charged ligands, Aß40-cut-peptide, and synthetic inhibitor ligands, in their selective coupling to Aß40 peptides and their fibrils. The simulations reveal that only Aß40-cut-peptide-covered NPs have strong and selective coupling to Aß40 monomers. On the other hand, positive, positive-neutral, Janus, and peptide NPs couple to the beta sheet surfaces of Aß40 fibrils and only the negative-neutral NPs couple to the fibril tips.

Multistep nucleation of nanocrystals in aqueous solution.

The nucleation and growth of solids from solutions impacts many natural processes and is fundamental to applications in materials engineering and medicine. For a crystalline solid, the nucleus is a nanoscale cluster of ordered atoms that forms through mechanisms still poorly understood. In particular, it is unclear whether a nucleus forms spontaneously from solution via a single- or multiple-step process. Here, using in situ electron microscopy, we show how gold and silver nanocrystals nucleate from supersaturated aqueous solutions in three distinct steps: spinodal decomposition into solute-rich and solute-poor liquid phases, nucleation of amorphous nanoclusters within the metal-rich liquid phase, followed by crystallization of these amorphous clusters. Our ab initio calculations on gold nucleation suggest that these steps might be associated with strong gold-gold atom coupling and water-mediated metastable gold complexes. The understanding of intermediate steps in nuclei formation has important implications for the formation and growth of both crystalline and amorphous materials.

Elucidating Surface Ligand-Dependent Kinetic Enhancement of Proteolytic Activity at Surface-Modified Quantum Dots.

Combining biomolecules such as enzymes with nanoparticles has much to offer for creating next generation synergistically functional bionanomaterials. However, almost nothing is known about how these two disparate components interact at this critical biomolecular-materials interface to give rise to improved activity and emergent properties. Here we examine how the nanoparticle surface can influence and increase localized enzyme activity using a designer experimental system consisting of trypsin proteolysis acting on peptide-substrates displayed around semiconductor quantum dots (QDs). To minimize the complexity of analyzing this system, only the chemical nature of the QD surface functionalizing ligands were modified. This was accomplished by synthesizing a series of QD ligands that were either positively or negatively charged, zwitterionic, neutral, and with differing lengths. The QDs were then assembled with different ratios of dye-labeled peptide substrates and exposed to trypsin giving rise to progress curves that were monitored by Förster resonance energy transfer (FRET). The resulting trypsin activity profiles were analyzed in the context of detailed molecular dynamics simulations of key interactions occurring at this interface. Overall, we find that a combination of factors can give rise to a localized activity that was 35-fold higher than comparable freely diffusing enzyme-substrate interactions. Contributing factors include the peptide substrate being prominently displayed extending from the QD surface and not sterically hindered by the longer surface ligands in conjunction with the presence of electrostatic and other productive attractive forces between the enzyme and the QD surface. An intimate understanding of such critical interactions at this interface can produce a set of guidelines that will allow the rational design of next generation high-activity bionanocomposites and theranostics.

Tuning the Selectivity of Dendron Micelles Through Variations of the Poly(ethylene glycol) Corona.

Engineering controllable cellular interactions into nanoscale drug delivery systems is key to enable their full potential. Here, using folic acid (FA) as a model targeting ligand and dendron micelles (DM) as a nanoparticle (NP) platform, we present a comprehensive experimental and modeling investigation of the structural properties of DMs that govern the formation of controllable, FA-mediated cellular interactions. Our experimental results demonstrate that a high level of control over the specific cell interactions of FA-targeted DMs can be achieved through modulation of the PEG corona length and the FA content. Using various molecular weight PEGs (0.6K, 1K, and 2K g/mol) and contents of dendron-FA conjugate incorporated into DMs (0, 5, 10, 25 wt %), the cell interactions of the targeted DMs could be controlled to exhibit minimal to >25-fold enhancement over nontargeted DMs. Molecular dynamics simulations indicated that structural characteristics, such as solvent accessible surface area of FA, local PEG density near FA, and FA mobility, account in part for the experimental differences in cellular interactions. The molecular structure that allows FA to depart from the surface of DMs to facilitate the initial cell surface binding was revealed to be the most important contributor for determining FA-mediated cellular interactions of DMs. The modular properties of DMs in controlling their specific cell interactions support the potential of DMs as a delivery platform and offer design cues for future development of targeted NPs.

Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks.

The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution.

Confined, Oriented, and Electrically Anisotropic Graphene Wrinkles on Bacteria.

Curvature-induced dipole moment and orbital rehybridization in graphene wrinkles modify its electrical properties and induces transport anisotropy. Current wrinkling processes are based on contraction of the entire substrate and do not produce confined or directed wrinkles. Here we show that selective desiccation of a bacterium under impermeable and flexible graphene via a flap-valve operation produces axially aligned graphene wrinkles of wavelength 32.4-34.3 nm, consistent with modified Föppl-von Kármán mechanics (confinement ∼0.7 × 4 µm(2)). Further, an electrophoretically oriented bacterial device with confined wrinkles aligned with van der Pauw electrodes was fabricated and exhibited an anisotropic transport barrier (ΔE = 1.69 meV). Theoretical models were developed to describe the wrinkle formation mechanism. The results obtained show bio-induced production of confined, well-oriented, and electrically anisotropic graphene wrinkles, which can be applied in electronics, bioelectromechanics, and strain patterning.

Charged group surface accessibility determines micelleplexes formation and cellular interaction.

Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The model micelle system was formed from methoxy-poly(ethylene glycol)-b-poly(lactide) (mPEG-PLA) mixed with methoxy-poly(ethylene glycol)-b-poly(lactide)-b-oligoarginine (mPEG-PLA-Rx, x = 8 or 15). Surface properties of the micelles were varied by controlling the oligoarginine block length and conjugation density. Micelles were observed to have a core-shell conformation in the aqueous environment where the PLA block constituted the hydrophobic core, mPEG and oligoarginine formed a hydrophilic corona. Significantly different thermodynamic behaviors were observed during the interaction of single stranded miRNA with micelles of different surface properties, and the resulting micelleplexes mediated substantial cellular association. Depending upon the oligoarginine length and density, micelles exhibited miRNA loading capacity directly related to the presentation of charged groups on the surface. The effect of charged group accessibility of cationic micelle on micelleplex properties provides guidance on future miRNA delivery system design.

Poly(ethylene glycol) Corona Chain Length Controls End-Group-Dependent Cell Interactions of Dendron Micelles.

To systematically investigate the relationship among surface charge, PEG chain length, and nano-bio interactions of dendron-based micelles (DMs), a series of PEGylated DMs with various end groups (-NH2, -Ac, and -COOH) and PEG chain lengths (600 and 2000 g/mol) are prepared and tested in vitro. The DMs with longer PEG chains (DM2K) do not interact with cells despite their positively charged surfaces. In sharp contrast, the DMs with shorter PEG chains (DM600) exhibit charge-dependent cellular interactions, as observed in both in vitro and molecular dynamics (MD) simulation results. Furthermore, all DMs with different charges display enhanced stability for hydrophobic dye encapsulation compared to conventional linear-block copolymer-based micelles, by allowing only a minimal leakage of the dye in vitro. Our results demonstrate the critical roles of the PEG chain length and polymeric architecture on the terminal charge effect and the stability of micelles, which provides an important design cue for polymeric micelles.