Coupling of SARS-CoV-2 to Aß Amyloid Fibrils.

The COVID-19 infection has been more problematic for individuals with certain health predispositions. Coronaviruses could also interfere with neural diseases if the viruses succeed in entering the brain. Therefore, it might be of principal interest to examine a possible coupling of coronaviruses and amyloid fibrils. Here, molecular dynamics simulations were used to investigate direct coupling of SARS-CoV-2 and Aß fibrils, which play a central role in neural diseases. The simulations revealed several stable binding configurations and their dynamics of Aß42 fibrils attached to spike proteins of the Omicron and Alpha variants of SARS-CoV-2.

Antiviral fibrils of self-assembled peptides with tunable compositions.

The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized ß-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability.

Nickel as a modifier of calcium oxalate: an in situ liquid cell TEM investigation of nucleation and growth.

Despite extensive research on the nucleation and growth of calcium oxalate (CaOx) crystals, there are still several challenges and unknowns that remain. In particular, the role of trace metal elements in the promotion or inhibition of CaOx crystals is not well understood. In the present study, in situ graphene liquid cell transmission electron microscopy (in situ GLC TEM) was used to observe real-time, nanoscale transformations of CaOx crystals in the presence of nickel ions (Ni2+). The results showed that Ni2+ form Ni-water complexes, acting as a shape-directing species, generating a unique morphology and altering growth kinetics. Transient adsorption of Ni-water complexes resulted in a metastable phase formation of calcium oxalate trihydrate. Atomistic molecular dynamics simulations confirmed that Ni2+ acts as a weak inhibitor which slows down the CaOx crystallization, elucidating that Ni2+ impacts small-sized CaOx clusters by bringing more water into the clusters. This work highlighted the intricacies behind the effect of Ni2+ on CaOx biomineralization that were made possible to discern using in situ GLC TEM.

Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks.

Though thiols are exceptionally versatile, their high reactivity has also hindered the synthesis and characterization of well-defined thiol-containing porous materials. Leveraging the mild conditions of the noncovalent peptide assembly, we readily synthesized and characterized a number of frameworks with thiols displayed at many unique positions and in several permutations. Importantly, nearly all assemblies were structurally determined using single-crystal X-ray diffraction to reveal their rich sequence-structure landscape and the cooperative noncovalent interactions underlying their assembly. These observations and supporting molecular dynamics calculations enabled rational engineering by the positive and negative design of noncovalent interactions. Furthermore, the thiol-containing frameworks undergo diverse single-crystal-to-single-crystal reactions, including toxic metal ion coordination (e.g., Cd2+, Pb2+, and Hg2+), selective uptake of Hg2+ ions, and redox transformations. Notably, we find a framework that supports thiol-nitrosothiol interconversion, which is applicable for biocompatible nitric oxide delivery. The modularity, ease of synthesis, functionality, and well-defined nature of these peptide-based thiol frameworks are expected to accelerate the design of complex materials with reactive active sites.

Unidirectional rotation of micromotors on water powered by pH-controlled disassembly of chiral molecular crystals.

Biological and synthetic molecular motors, fueled by various physical and chemical means, can perform asymmetric linear and rotary motions that are inherently related to their asymmetric shapes. Here, we describe silver-organic micro-complexes of random shapes that exhibit macroscopic unidirectional rotation on water surface through the asymmetric release of cinchonine or cinchonidine chiral molecules from their crystallites asymmetrically adsorbed on the complex surfaces. Computational modeling indicates that the motor rotation is driven by a pH-controlled asymmetric jet-like Coulombic ejection of chiral molecules upon their protonation in water. The motor is capable of towing very large cargo, and its rotation can be accelerated by adding reducing agents to the water.

High Pressure Torsion of Copper; Effect of Processing Temperature on Structural Features, Microhardness and Electric Conductivity.

By optimizing the fabrication method, copper components featuring (typically contradicting) advantageous electric conductivity and favorable mechanical properties can be acquired. In this study, we subjected conventional electroconductive copper to a single revolution of high pressure torsion (HPT) at room temperature (RT), searched for the conditions which would yield comparable structure characteristics (grain size) when deformed at a cryogenic temperature, and finally compared the mechanical and electric behaviors to assess specific differences and correlate them with the (sub)structural development. 180° revolution of cryo-HPT imparted structure refinement comparable to 360° revolution of room temperature HPT, i.e., the average grain size at the periphery of both the specimens was ~7 µm. The 360° RT HPT specimen exhibited preferential (111)||SD (shear direction) texture fiber in all the examined regions, whereas the 180° cryo-HPT specimen exhibited more or less randomly oriented grains of equiaxed shapes featuring substantial substructure development of a relatively homogeneous character and massive occurrence of (nano)twins. These structural features resulted in the increase in microhardness to the average value of 118.2 HV0.2 and the increase in the electric conductivity to 59.66 MS·m-1 (compared to 105 HV0.2 and 59.14 MS·m-1 acquired for the 360° RT HPT specimen). The deformation under the cryogenic conditions also imparted higher homogeneity of microhardness distribution when compared to RT processing.

Bioinspired Separator with Ion-Selective Nanochannels for Lithium Metal Batteries.

The free transport of anions through commercial polyolefin separators used in lithium metal batteries (LMBs) gives rise to concentration polarization and rapid growth of lithium dendrites, leading to poor performance and short circuits. Here, a new poly(ethylene-co-acrylic acid) (EAA) separator with functional active sites (i.e., carboxyl groups) distributing along the pore surface was fabricated, forming bioinspired ion-conducting nanochannels within the separator. As the carboxyl groups effectively desolvated Li+ and immobilized anion, the as-prepared EAA separator selectively accelerated the transport of Li+ with transference number of Li+ (tLi+) up to 0.67, which was further confirmed by molecular dynamics simulations. The battery with the EAA separator can be stably cycled over 500 h at 5 mA cm-2. The LMBs with the EAA separator have exceptional electrochemical performance of 107 mAh g-1 at 5 C and a capacity retention of 69% after 200 cycles. This work provides new commercializable separators toward dendrite-free LMBs.

Scalable Inhibitors of the Nsp3-Nsp4 Coupling in SARS-CoV-2.

The human Betacoronavirus SARS-CoV-2 is a novel pathogen claiming millions of lives and causing a global pandemic that has disrupted international healthcare systems, economies, and communities. The virus is fast mutating and presenting more infectious but less lethal versions. Currently, some small-molecule therapeutics have received FDA emergency use authorization for the treatment of COVID-19, including Lagevrio (molnupiravir) and Paxlovid (nirmaltrevir/ritonavir), which target the RNA-dependent RNA polymerase and the 3CLpro main protease, respectively. Proteins downstream in the viral replication process, specifically the nonstructural proteins (Nsps1-16), are potential drug targets due to their crucial functions. Of these Nsps, Nsp4 is a particularly promising drug target due to its involvement in the SARS-CoV viral replication and double-membrane vesicle formation (mediated via interaction with Nsp3). Given the degree of sequence conservation of these two Nsps across the Betacoronavirus clade, their protein-protein interactions and functions are likely to be conserved as well in SARS-CoV-2. Through AlphaFold2 and its recent advancements, protein structures were generated of Nsp3 and 4 lumenal loops of interest. Then, using a combination of molecular docking suites and an existing library of lead-like compounds, we virtually screened 7 million ligands to identify five putative ligand inhibitors of Nsp4, which could present an alternative pharmaceutical approach against SARS-CoV-2. These ligands exhibit promising lead-like properties (ideal molecular weight and log P profiles), maintain fixed-Nsp4-ligand complexes in molecular dynamics (MD) simulations, and tightly associate with Nsp4 via hydrophobic interactions. Additionally, alternative peptide inhibitors based on Nsp3 were designed and shown in MD simulations to provide a highly stable binding to the Nsp4 protein. Finally, these therapeutics were attached to dendrimer structures to promote their multivalent binding with Nsp4, especially its large flexible luminal loop (Nsp4LLL). The therapeutics tested in this study represent many different approaches for targeting large flexible protein structures, especially those localized to the ER. This study is the first work targeting the membrane rearrangement system of viruses and will serve as a potential avenue for treating viruses with similar replicative function.

Unveiling growth and dynamics of liposomes by graphene liquid cell-transmission electron microscopy.

Liposome is a model system for biotechnological and biomedical purposes spanning from targeted drug delivery to modern vaccine research. Yet, the growth mechanism of liposomes is largely unknown. In this work, the formation and evolution of phosphatidylcholine-based liposomes are studied in real-time by graphene liquid cell-transmission electron microscopy (GLC-TEM). We reveal important steps in the growth, fusion and denaturation of phosphatidylcholine (PC) liposomes. We show that initially complex lipid aggregates resembling micelles start to form. These aggregates randomly merge while capturing water and forming small proto-liposomes. The nanoscopic containers continue sucking water until their membrane becomes convex and free of redundant phospholipids, giving stabilized PC liposomes of different sizes. In the initial stage, proto-liposomes grow at a rate of 10-15 nm s-1, which is followed by their growth rate of 2-5 nm s-1, limited by the lipid availability in the solution. Molecular dynamics (MD) simulations are used to understand the structure of micellar clusters, their evolution, and merging. The liposomes are also found to fuse through lipid bilayers docking followed by the formation of a hemifusion diaphragm and fusion pore opening. The liposomes denaturation can be described by initial structural destabilization and deformation of the membrane followed by the leakage of the encapsulated liquid. This study offers new insights on the formation and growth of lipid-based molecular assemblies which is applicable to a wide range of amphiphilic molecules.

Dendrimer-Peptide Conjugates for Effective Blockade of the Interactions between SARS-CoV-2 Spike Protein and Human ACE2 Receptor.

The coronavirus disease 2019 (COVID-19) pandemic has threatened the stability of global healthcare, which is becoming an endemic issue. Despite the development of various treatment strategies to fight COVID-19, the currently available treatment options have shown varied efficacy. Herein, we have developed an avidity-based SARS-CoV-2 antagonist using dendrimer-peptide conjugates (DPCs) for effective COVID-19 treatment. Two different peptide fragments obtained from angiotensin-converting enzyme 2 (ACE2) were integrated into a single sequence, followed by the conjugation to poly(amidoamine) (PAMAM) dendrimers. We hypothesized that the strong multivalent binding avidity endowed by dendrimers would help peptides effectively block the interaction between SARS-CoV-2 and ACE2, and this antagonist effect would be dependent upon the generation (size) of the dendrimers. To assess this, binding kinetics of the DPCs prepared from generation 4 (G4) and G7 PAMAM dendrimers to spike protein of SARS-CoV-2 were quantitatively measured using surface plasmon resonance. The larger dendrimer-based DPCs exhibited significantly enhanced binding strength by 3 orders of magnitude compared to the free peptides, whereas the smaller one showed a 12.8-fold increase only. An in vitro assay using SARS-CoV-2-mimicking microbeads also showed the improved SARS-CoV-2 blockade efficiency of the G7-peptide conjugates compared to G4. In addition, the interaction between the DPCs and SARS-CoV-2 was analyzed using molecular dynamics (MD) simulation, providing an insight into how the dendrimer-mediated multivalent binding effect can enhance the SARS-CoV-2 blockade. Our findings demonstrate that the DPCs having strong binding to SARS-CoV-2 effectively block the interaction between ACE2 and SARS-CoV-2, providing a potential as a high-affinity drug delivery system to direct anti-COVID payloads to the virus.

Linear One-Dimensional Assembly of Metal Nanostructures onto an Asymmetric Peptide Nanofiber with High Persistence Length.

Self-assembled peptide fibrils have been used extensively to template the organization of metal nanoparticles in a one-dimensional (1D) array. It has been observed that the formation of the 1D arrays with a width of a single or few nanoparticles (viz. 20 nm diameter) is only possible if the templating fibers have comparable diameters (viz. ≤20 nm). Accordingly, until today, all the peptide-based templates enabling such 1D arrays have very low persistence lengths, a property that depends strongly on the diameter of the template, owing to the inherent flexibility of only a few nanometer-wide fibers. Here, we demonstrate the formation of high persistence length 1D arrays templated by a short self-assembling peptide fibril with an asymmetrically distributed charged surface. The asymmetric nature of the peptide fibril allows charge-dependent deposition of the nanoparticles only to the part of the fiber with complementary charges, and the rest of the fibril surface remains free of nanoparticles. Consequently, fibers with a much higher diameter, which will have a higher persistence length, are able to template single or few nanoparticle-wide 1D arrays. Detailed microscopy, molecular dynamics simulations, and crystal structure analysis provide molecular-level insights into fiber asymmetry and its interactions with diverse nanostructures such as gold and magnetic nanoparticles. This study will afford an alternative paradigm for high persistence length 1D array fabrication comparable to DNA nanotechnology and lithography but with tremendous cost-effectiveness.

Broad-Spectrum Extracellular Antiviral Properties of Cucurbit[n]urils.

Viruses are microscopic pathogens capable of causing disease and are responsible for a range of human mortalities and morbidities worldwide. They can be rendered harmless or destroyed with a range of antiviral chemical compounds. Cucurbit[n]urils (CB[n]s) are a family of macrocycle chemical compounds existing as a range of homologues; due to their structure, they can bind to biological materials, acting as supramolecular "hosts" to "guests", such as amino acids. Due to the increasing need for a nontoxic antiviral compound, we investigated whether cucurbit[n]urils could act in an antiviral manner. We have found that certain cucurbit[n]uril homologues do indeed have an antiviral effect against a range of viruses, including herpes simplex virus 2 (HSV-2), respiratory syncytial virus (RSV) and SARS-CoV-2. In particular, we demonstrate that CB[7] is the active homologue of CB[n], having an antiviral effect against enveloped and nonenveloped species. High levels of efficacy were observed with 5 min contact times across different viruses. We also demonstrate that CB[7] acts with an extracellular virucidal mode of action via host-guest supramolecular interactions between viral surface proteins and the CB[n] cavity, rather than via cell internalization or a virustatic mechanism. This finding demonstrates that CB[7] acts as a supramolecular virucidal antiviral (a mechanism distinct from other current extracellular antivirals), demonstrating the potential of supramolecular interactions for future antiviral disinfectants.

Elucidating the Impact of Hydrophilic Segments on 19F MRI Sensitivity of Fluorinated Block Copolymers.

A major challenge in the preparation of polymeric 19F magnetic resonance imaging (MRI) contrast agents (CAs) is signal attenuation caused by reduced segmental mobility of partly fluorinated polymers possessing large numbers of fluorine atoms. Previous studies have thus mainly focused on the development of fluorinated segments for improved 19F MRI; however, detailed investigations of the role of hydrophilic segments on imaging performance remain scarce. In this study, three hydrophilic and biocompatible monomers, i.e., 2-(methylsulfinyl)ethyl acrylate (MSEA), oligo(ethylene glycol) methyl ether acrylate (OEGA), and oligo(2-methyl-2-oxazoline) acrylate (OMOXA), were used to prepare perfluoropolyether (PFPE)-containing amphiphilic block polymers through reversible addition-fragmentation chain-transfer (RAFT) polymerization. The effect of the different hydrophilic segments on 19F imaging performance was explored. The three polymers could be readily dissolved in aqueous solutions, forming assemblies with the hydrophobic PFPE as the core and the hydrophilic chains as the shell. Molecular dynamics simulations demonstrate that the POMOXA chains adopt a rigid, extended conformation, leading to a relatively short 19F NMR spin-spin relaxation time (T2), lower NMR detectable 19F spins (i.e., visibility), and the least intense 19F MRI signal. In contrast, although PMSEA-PFPE has a shorter 19F NMR T2 than POEGA-PFPE, the much higher 19F spin visibility enhances its MRI signal intensity. The result confirms the importance of maintaining both high fluorine visibility and long T2 relaxation time to prepare effective CAs and highlight the key role of the nonfluorinated hydrophilic segments in determining these parameters.

Ultra-stable all-solid-state sodium metal batteries enabled by perfluoropolyether-based electrolytes.

Rechargeable batteries paired with sodium metal anodes are considered to be one of the most promising high-energy and low-cost energy-storage systems. However, the use of highly reactive sodium metal and the formation of sodium dendrites during battery operation have caused safety concerns, especially when highly flammable liquid electrolytes are used. Here we design and develop solvent-free solid polymer electrolytes (SPEs) based on a perfluoropolyether-terminated polyethylene oxide (PEO)-based block copolymer for safe and stable all-solid-state sodium metal batteries. Compared with traditional PEO SPEs, our results suggest that block copolymer design allows for the formation of self-assembled nanostructures leading to high storage modulus at elevated temperatures with the PEO domains providing transport channels even at high salt concentration (ethylene oxide/sodium = 8/2). Moreover, it is demonstrated that the incorporation of perfluoropolyether segments enhances the Na+ transference number of the electrolyte to 0.46 at 80 °C and enables a stable solid electrolyte interface. The new SPE exhibits highly stable symmetric cell-cycling performance at high current density (0.5 mA cm-2 and 1.0 mAh cm-2, up to 1,000 h). Finally, the assembled all-solid-state sodium metal batteries demonstrate outstanding capacity retention, long-term charge/discharge stability (Coulombic efficiency, 99.91%; >900 cycles with Na3V2(PO4)3 cathode) and good capability with high loading NaFePO4 cathode (>1 mAh cm-2).

Bimodal liquid biopsy for cancer immunotherapy based on peptide engineering and nanoscale analysis.

Despite its high potential, PD-L1 expressed by tumors has not been successfully utilized as a biomarker for estimating treatment responses to immunotherapy. Circulating tumor cells (CTCs) and tumor-derived exosomes that express PD-L1 can potentially be used as biomarkers; however, currently available assays lack clinically significant sensitivity and specificity. Here, a novel peptide-based capture surface is developed to effectively isolate PD-L1-expressing CTCs and exosomes from human blood. For the effective targeting of PD-L1, this study integrates peptide engineering strategies to enhance the binding strength and specificity of a ß-hairpin peptide derived from PD-1 (pPD-1). Specifically, this study examines the effect of poly(ethylene glycol) spacers, the secondary peptide structure, and modification of peptide sequences (e.g., removal of biologically redundant amino acid residues) on capture efficiency. The optimized pPD-1 configuration captures PD-L1-expressing tumor cells and tumor-derived exosomes with 1.5-fold (p = 0.016) and 1.2-fold (p = 0.037) higher efficiencies, respectively, than their whole antibody counterpart (aPD-L1). This enhanced efficiency is translated into more clinically significant detection of CTCs (1.9-fold increase; p = 0.035) and exosomes (1.5-fold increase; p = 0.047) from patients' baseline samples, demonstrating stronger correlation with patients' treatment responses. Additionally, we confirmed that the clinical accuracy of our system can be further improved by co-analyzing the two biomarkers (bimodal CTC/exosome analysis). These data demonstrate that pPD-1-based capture is a promising approach for capturing PD-L1-expressing CTCs and exosomes, which can be used as a reliable biomarker for cancer immunotherapy.

Influence of Cryo-Processing and Post-SPD Annealing on Creep Behavior of CP Titanium.

The commercial purity of VT1-0 titanium was processed by the rolling process and executed at elevated, room, and cryo-temperatures. These processings led to the formation of an ultrafine-grained microstructure, with the mean grain size at a nanometer level. Some of these materials were statically annealed at a temperature of 823 K for 1 h, which led to significant subgrains and grain coarsening. The constant load creep tests in tension were carried out in argon on all states of materials, at temperatures of 648-723 K and different ranges of applied stresses. From the value of the steady-state creep rate, the control creep mechanisms were determined. The microstructure analyses were carried out via SEM and TEM. It was found that titanium prepared at elevated and room temperatures have a higher creep strength than titanium prepared at cryo-temperatures. Furthermore, the post-SPD -annealing led to a significant decrease in the creep properties. The influence of the preparation temperature on the difference of the creep behavior were discussed and explained using the microstructure analyses of the tests' samples.

Creep Resistance of S304H Austenitic Steel Processed by High-Pressure Sliding.

Sheets of coarse-grained S304H austenitic steel were processed by high-pressure sliding (HPS) at room temperature and a ultrafine-grained microstructure with a mean grain size of about 0.14 µm was prepared. The microstructure changes and creep behavior of coarse-grained and HPS-processed steel were investigated at 500-700 °C under the application of different loads. It was found that the processing of S304H steel led to a significant improvement in creep strength at 500 °C. However, a further increase in creep temperature to 600 °C and 700 °C led to the deterioration of creep behavior of HPS-processed steel. The microstructure results suggest that the creep behavior of HPS-processed steel is associated with the thermal stability of the SPD-processed microstructure. The recrystallization, grain growth, the coarsening of precipitates led to a reduction in creep strength of the HPS-processed state. It was also observed that in the HPS-processed microstructure the fast formation of σ-phase occurs. The σ-phase was already formed during slight grain coarsening at 600 °C and its formation was enhanced after recrystallization at 700 °C.

Inhibitor-Mediated Structural Transition in a Minimal Amyloid Model.

Despite the fundamental clinical importance of amyloid fibril formation, its mechanism is still enigmatic. Crystallography of minimal amyloid models was a milestone in the understanding of the architecture and biological activities of amyloid fibers. However, the crystal structure of ultimate dipeptide-based amyloids is not yet reported. Herein, we present the crystal structure of a typical amyloid-forming minimal dipeptide, Ac-Phe-Phe-NH2 (Ac-FF-NH2 ), showing a canonical ß-sheet structure at the atomic level. The simplicity of the structure helped in investigating amyloid-inhibition using crystallography, never previously reported for larger peptide models. Interestingly, in the presence of an inhibitor, the supramolecular packing of Ac-FF-NH2 molecules rearranged into a supramolecular 2-fold helix (21 helix). This study promotes our understanding of the mechanism of amyloid formation and of the structural transitions that occur during the inhibition process in a most fundamental model.

Hierarchically Multivalent Peptide-Nanoparticle Architectures: A Systematic Approach to Engineer Surface Adhesion.

The multivalent binding effect has been the subject of extensive studies to modulate adhesion behaviors of various biological and engineered systems. However, precise control over the strong avidity-based binding remains a significant challenge. Here, a set of engineering strategies are developed and tested to systematically enhance the multivalent binding of peptides in a stepwise manner. Poly(amidoamine) (PAMAM) dendrimers are employed to increase local peptide densities on a substrate, resulting in hierarchically multivalent architectures (HMAs) that display multivalent dendrimer-peptide conjugates (DPCs) with various configurations. To control binding behaviors, effects of the three major components of the HMAs are investigated: i) poly(ethylene glycol) (PEG) linkers as spacers between conjugated peptides; ii) multiple peptides on the DPCs; and iii) various surface arrangements of HMAs (i.e., a mixture of DPCs each containing different peptides vs DPCs cofunctionalized with multiple peptides). The optimized HMA configuration enables significantly enhanced target cell binding with high selectivity compared to the control surfaces directly conjugated with peptides. The engineering approaches presented herein can be applied individually or in combination, providing guidelines for the effective utilization of biomolecular multivalent interactions using DPC-based HMAs.