Entangling of Peptide Nanofibers Reduces the Invasiveness of SARS-CoV-2.

The viral spike (S) protein on the surface of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to angiotensin-converting enzyme 2 (ACE2) receptors on the host cells, facilitating its entry and infection. Here, functionalized nanofibers targeting the S protein with peptide sequences of IRQFFKK, WVHFYHK and NSGGSVH, which are screened from a high-throughput one-bead one-compound screening strategy, are designed and prepared. The flexible nanofibers support multiple binding sites and efficiently entangle SARS-CoV-2, forming a nanofibrous network that blocks the interaction between the S protein of SARS-CoV-2 and the ACE2 on host cells, and efficiently reduce the invasiveness of SARS-CoV-2. In summary, nanofibers entangling represents a smart nanomedicine for the prevention of SARS-CoV-2.

New Biocompatible Nanohydrogels of Predefined Sizes for Complexing Nucleic Acids.

The advent of protein expression using m-RNA applied lately for treating the COVID pandemic, and gene editing using CRISPR/Cas9 technology for introducing DNA sequences at a specific site in the genome, are milestones for the urgent need of developing new nucleic acid delivery systems with improved delivery properties especially for in vivo applications. We have designed, synthesized, and characterized novel cross-linked monodispersed nanohydrogels (NHG's) with well-defined sizes ranging between 50-400 nm. The synthesis exploits the formation of self-assemblies generated upon heating a thermo-responsive mixture of monomers. Self-assemblies are formed and polymerized at high temperatures resulting in NHGs with sizes that are predetermined by the sizes of the intermediate self-assemblies. The obtained NHGs were chemically reduced to lead particles with highly positive zeta potential and low cell toxicity. The NHGs form complexes with DNA, and at optimal charge ratio the size of the complexes is concomitant with the size of the NHG's. Thus, the DNA is fully embedded inside the NHGs. The new NHGs and their DNA complexes are devoid of cell toxicity which together with their tunned sizes, make them potential tools for gene delivery and foreign protein expression.

Hybrid Peptide–Agarose Hydrogels for 3D Immunoassays

Recent advances in biosensing analytical platforms have brought relevant outcomes for novel diagnostic and therapy-oriented applications. In this context, 3D droplet microarrays, where hydrogels are used as matrices to stably entrap biomolecules onto analytical surfaces, potentially provide relevant advantages over conventional 2D assays, such as increased loading capacity, lower nonspecific binding, and enhanced signal-to-noise ratio. Here, we describe a hybrid hydrogel composed of a self-assembling peptide and commercial agarose (AG) as a suitable matrix for 3D microarray bioassays. The hybrid hydrogel is printable and self-adhesive and allows analyte diffusion. As a showcase example, we describe its application in a diagnostic immunoassay for the detection of SARS-CoV-2 infection. © 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

DNA origami traps for large viruses

Virus-enveloping macromolecular shells or tilings can prevent viruses from entering cells. Here, we describe the design and assembly of a cone-shaped DNA origami higher-order assembly that can engulf and tile the surface of pleomorphic virus samples larger than 100 nm. We determine the structures of subunits and of complete cone assemblies using cryoelectron microscopy (cryo-EM) and establish stabilization treatments to enable usage in in vivo conditions. We use the cones exemplarily to engulf influenza A virus particles and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), chikungunya, and Zika virus-like particles. Depending on the relative dimensions of cone to virus particles, multiple virus particles may be trapped per single cone, and multiple cones can also tile and adapt to the surface of aspherical virus particles. The cone assemblies form with high yields, require little purification, and are amenable for mass production, which is a key requirement for future real-world uses including as a potential antiviral agent. © 2022 The Authors

Ultrashort Peptides for the Self-Assembly of an Antiviral Coating

Antiviral compounds are important for generating sterile surfaces. Here, two extremely short peptides, DOPA-Phe-NH2 and DOPA-Phe(4F)-NH2 that can self-assemble into spherical nanoparticles with antiviral activity are presented. The peptide assemblies possess excellent antiviral activity against bacteriophage T4 with antiviral minimal inhibitory concentrations of 125 and 62.5 µg mL−1, for DOPA-Phe-NH2 and DOPA-Phe(4F)-NH2, respectively. When the peptide assemblies are applied on a glass substrate by drop-casting, they deactivate more than 99.9% of bacteriophage T4 and Canine coronavirus. Importantly, the peptide assemblies have low toxicity toward mammalian cells. Overall, the findings can provide a novel strategy for the design and development of antiviral coatings for a decreased risk of viral infections. © 2023 The Authors. Advanced Materials Interfaces published by Wiley-VCH GmbH.

A Multivalent and Thermostable Nanobody Neutralizing SARS-CoV-2 Omicron (B.1.1.529).

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants have risen to dominance, which contains far more mutations in the spike protein in comparison to previously reported variants, compromising the efficacy of most existing vaccines or therapeutic monoclonal antibodies. Nanobody screened from high-throughput naïve libraries is a potential candidate for developing preventive and therapeutic antibodies. Methods: Four nanobodies specific to the SARS-CoV-2 wild-type receptor-binding domain (RBD) were screened from a naïve phage display library. Their affinity and neutralizing activity were evaluated by surface plasmon resonance assays, surrogate virus neutralization tests, and pseudovirus neutralization assays. Preliminary identification of the binding epitopes of nanobodies by peptide-based ELISA and competition assay. Then four multivalent nanobodies were engineered by attaching the monovalent nanobodies to an antibody-binding nanoplatform constructed based on the lumazine synthase protein cage nanoparticles isolated from the Aquifex aeolicus (AaLS). Finally, the differences in potency between the monovalent and multivalent nanobodies were compared using the same methods. Results: Three of the four specific nanobodies could maintain substantial inhibitory activity against the Omicron (B.1.1.529), of them, B-B2 had the best neutralizing activity against the Omicron (B.1.1.529) pseudovirus (IC50 = 1.658 µg/mL). The antiviral ability of multivalent nanobody LS-B-B2 was improved in the Omicron (B.1.1.529) pseudovirus assays (IC50 = 0.653 µg/mL). The results of peptide-based ELISA indicated that LS-B-B2 might react with the linear epitopes in the SARS-CoV-2 RBD conserved regions, which would clarify the mechanisms for the maintenance of potent neutralization of Omicron (B.1.1.529) preliminary. Conclusion: Our study indicated that the AaLS could be used as an antibody-binding nanoplatform to present nanobodies on its surface and improve the potency of nanobodies. The multivalent nanobody LS-B-B2 may serve as a potential agent for the neutralization of SARS-CoV-2 variants.

Vaccination Strategies Based on Bacterial Self-Assembling Proteins as Antigen Delivery Nanoscaffolds.

Vaccination has saved billions of human lives and has considerably reduced the economic burden associated with pandemic and endemic infectious diseases. Notwithstanding major advancements in recent decades, multitude diseases remain with no available effective vaccine. While subunit-based vaccines have shown great potential to address the safety concerns of live-attenuated vaccines, their limited immunogenicity remains a major drawback that still needs to be addressed for their use fighting infectious illnesses, autoimmune disorders, and/or cancer. Among the adjuvants and delivery systems for antigens, bacterial proteinaceous supramolecular structures have recently received considerable attention. The use of bacterial proteins with self-assembling properties to deliver antigens offers several advantages, including biocompatibility, stability, molecular specificity, symmetrical organization, and multivalency. Bacterial protein nanoassemblies closely simulate most invading pathogens, acting as an alarm signal for the immune system to mount an effective adaptive immune response. Their nanoscale architecture can be precisely controlled at the atomic level to produce a variety of nanostructures, allowing for infinite possibilities of organized antigen display. For the bottom-up design of the proteinaceous antigen delivery scaffolds, it is essential to understand how the structural and physicochemical properties of the nanoassemblies modulate the strength and polarization of the immune responses. The present review first describes the relationships between structure and the generated immune responses, before discussing potential and current clinical applications.

Modular Metal-Quinone Networks with Tunable Architecture and Functionality.

Nanostructured materials with tunable structures and functionality are of interest in diverse areas. Herein, metal ions are coordinated with quinones through metal-acetylacetone coordination bonds to generate a class of structurally tunable, universally adhesive, hydrophilic, and pH-degradable materials. A library of metal-quinone networks (MQNs) is produced from five model quinone ligands paired with nine metal ions, leading to the assembly of particles, tubes, capsules, and films. Importantly, MQNs show bidirectional pH-responsive disassembly in acidic and alkaline solutions, where the quinone ligands mediate the disassembly kinetics, enabling temporal and spatial control over the release of multiple components using multilayered MQNs. Leveraging this tunable release and the inherent medicinal properties of quinones, MQN prodrugs with a high drug loading (>89 wt %) are engineered using doxorubicin for anti-cancer therapy and shikonin for the inhibition of the main protease in the SARS-CoV-2 virus.

DNA origami traps for large viruses

Summary Virus-enveloping macromolecular shells or tilings can prevent viruses from entering cells. Here, we describe the design and assembly of a cone-shaped DNA origami higher-order assembly that can engulf and tile the surface of pleomorphic virus samples larger than 100 nm. We determine the structures of subunits and of complete cone assemblies using cryoelectron microscopy (cryo-EM) and establish stabilization treatments to enable usage in in vivo conditions. We use the cones exemplarily to engulf influenza A virus particles and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), chikungunya, and Zika virus-like particles. Depending on the relative dimensions of cone to virus particles, multiple virus particles may be trapped per single cone, and multiple cones can also tile and adapt to the surface of aspherical virus particles. The cone assemblies form with high yields, require little purification, and are amenable for mass production, which is a key requirement for future real-world uses including as a potential antiviral agent.

Recombinant Protein Micelles to Block Transduction by SARS-CoV-2 Pseudovirus.

The continuing emergence of variants of the SARS-CoV-2 virus requires the development of modular molecular therapies. Here, we engineered a recombinant amphiphilic protein, oleosin, to spontaneously self-assemble into multivalent micellar nanostructures which can block the Spike S1 protein of SARS-CoV-2 pseudoviruses (PVs). Short recombinant proteins like oleosin can be formulated more easily than antibodies and can be functionalized with precision through genetic engineering. We cloned S1-binding mini-protein genes called LCBx, previously designed by David Baker's laboratory (UW Seattle), to the N-terminus of oleosin, expressing Oleo-LCBx proteins in E. coli. These proteins largely formed 10-100 nm micelles as verified by dynamic light scattering. Two proteins, Oleo-LCB1 and Oleo-LCB3, were seen to completely and irreversibly block transduction by both wild-type and delta variant PVs into 293T-hsACE2 cells at 10 µM. Presented in multivalent micelles, these proteins reduced transduction by PVs down to a functional protein concentration of 5 nM. Additionally, Oleo-LCB1 micelles outperformed corresponding synthetic LCB1 mini-proteins in reducing transduction by PVs. Tunable aqueous solubility of recombinant oleosin allowed incorporation of peptides/mini-proteins at high concentrations within micelles, thus enhancing drug loading. To validate the potential multifunctionality of the micelles, we showed that certain combinations of Oleo-LCB1 and Oleo-LCB3 performed much better than the individual proteins at the same concentration. These micelles, which we showed to be non-toxic to human cells, are thus a promising step toward the design of modular, multifunctional therapeutics that could bind to and inactivate multiple receptors and proteins necessary for the infection of the SARS-CoV-2 virus.

Hybrid Peptide-Agarose Hydrogels for 3D Immunoassays

Recent advances in biosensing analytical platforms have brought relevant outcomes for novel diagnostic and therapy-oriented applications. In this context, 3D droplet microarrays, where hydrogels are used as matrices to stably entrap biomolecules onto analytical surfaces, potentially provide relevant advantages over conventional 2D assays, such as increased loading capacity, lower nonspecific binding, and enhanced signal-to-noise ratio. Here, we describe a hybrid hydrogel composed of a self-assembling peptide and commercial agarose (AG) as a suitable matrix for 3D microarray bioassays. The hybrid hydrogel is printable and self-adhesive and allows analyte diffusion. As a showcase example, we describe its application in a diagnostic immunoassay for the detection of SARS-CoV-2 infection.

Advances on nanoformulation approaches for delivering plant-derived antioxidants: A case of quercetin.

Oxidative stress has been implicated in tumorigenic, cardiovascular, neuro-, and age-related degenerative changes. Antioxidants minimize the oxidative damage through neutralization of reactive oxygen species (ROS) and other causative agents. Ever since the emergence of COVID-19, plant-derived antioxidants have received enormous attention, particularly in the Indian subcontinent. Quercetin (QCT), a bio-flavonoid, exists in the glycosylated form in fruits, berries and vegetables. The antioxidant potential of QCT analogs relates to the number of free hydroxyl groups in their structure. Despite presence of these groups, QCT exhibits substantial hydrophobicity. Formulation scientists have tested nanotechnology-based approaches for its improved solubilization and delivery to the intended site of action. By the virtue of its hydrophobicity, QCT gets encapsulated in nanocarriers carrying hydrophobic domains. Apart from passive accumulation, active uptake of such formulations into the target cells can be facilitated through well-studied functionalization strategies. In this review, we have discussed the approaches of improving solubilization and bioavailability of QCT with the use of nanoformulations.

Passivating the Omicron SARS-CoV-2 variant with self-assembled nano peptides: Specificity, stability, and no cytotoxicity

The SARS-CoV-2 Omicron variant is called a “variant of concern” (VOC) which has spread all over the world at a faster rate than even the first SARS-CoV-2 outbreak despite travel restrictions. In order to combat the health consequences from a SARS-CoV-2 Omicron variant infection, the objective of the present in vitro study was to develop self-assembled nano peptides to attach to the virus and inhibit its attachment and entry into mammalian cells for replication. For this purpose, two amphipathic peptides containing hydrophobic and hydrophilic peptides and an unnatural amino acid (such as 2-aminoisobutyric acid (U)) were designed to attach to the less mutated virus envelope rather than more frequently mutated S-protein region: NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK. These peptides were synthesized using the solid phase peptide synthesis method and were characterized for mammalian cell infection using well-established pseudo virus assays. In vitro results showed that the two self-assembled nano peptides significantly inhibited the ability of the SARS-CoV-2 Omicron variant virus to infect mammalian cells and replicate with IC50 values of 0.5 and 360 mg/ml for NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK, respectively. Most impressively, 1 mg/ml of NapFFTLUFLTUTEKKKK resulted in a 2 log reduction in pseudovirus replication after just 15 min at a viral load of 106 copies/ml. Results further confirmed that the peptides continued to passivate the SARS-CoV-2 Omicron variant for up to one week and were stable in cell culture media before being added to the virus. Mechanistically, in vitro results showed selective binding of the peptides to the SARS-CoV-2 Omicron variant envelop protein over the more frequently mutated spike protein up to one week demonstrating the stability of the peptides. Cytotoxicity studies with fibroblasts also showed no toxicity when exposed to the peptides for 72 h. In summary, the present results strongly suggest that the two peptides developed in this study should be further researched for a wide range of anti-SARS-CoV-2 virus applications, including the present Omicron and future mutations.

Bactericidal and Antiviral Bionic Metalized Nanocoatings.

In diverse living organisms, bionanocoatings provide multiple functionalities, to the surfaces they cover. We have, previously, identified the molecular mechanisms of Turing-based self-assembly of insect corneal nanocoatings and developed forward-engineering approaches to construct multifunctional soft bionic nanocoatings, encompassing the Drosophila protein Retinin. Here, we expand the versatility of the bionic nanocoatings, by identifying and using diverse Retinin-like proteins and different methods of their metallization, using nickel, silver, and copper ions. Comparative assessment, of the resulting bactericidal, antiviral, and cytotoxic properties, identifies the best protocols, to construct safe and anti-infective metalized bionic nanocoatings. Upscaled application of these protocols, to various public surfaces, may represent a safe and economic approach to limit hazardous infections.

Supramolecular Microtubes by Self‐Assembly of a Co–Drug and Antifungal Activities against Saccharomyces cerevisiae

Benzotriazole esters have been reported to work as inactivators for severe acute respiratory syndrome (SARS) 3CL protease. A calcium channel blocker m‐Nifedipine is well known for its effect in hypertension, as well as angina. Combining two, we have synthesized co‐drug m‐Nifedipine‐3‐benzotriazol‐1‐yl‐ester 1 which exhibited antifungal activities against Saccharomyces cerevisiae (S. cerevisiae strain BY4742). The single‐crystal X‐ray diffraction study shows that there are two molecules with opposite chirality in the asymmetric unit. Intramolecular π‐π stacking interactions stabilize the tripod shape compound 1 molecules. In higher‐order assembly, compound 1 molecules are assembled by intermolecular hydrogen bonding, maintaining a proper registry to form a supramolecular nanotube‐like structure. Moreover, compound 1 inhibits the growth of the Saccharomyces cerevisiae. The minimal inhibitory concentration (MIC) against the Saccharomyces cerevisiae was 10 μg/mL. The docking studies indicate that compound 1 has a strong affinity (binding energy −8.67 kcal/mol) for the enzyme lanosterol 14α‐demethylase of the Saccharomyces cerevisiae. The compound 1 binds to Leu58 and Ser50 of lanosterol 14α‐demethylase through intermolecular hydrogen bonding interactions. [ FROM AUTHOR] Copyright of ChemistrySelect is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Ambient Temperature Stable, Scalable COVID-19 Polymer Particle Vaccines Induce Protective Immunity.

There is an unmet need for safe and effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines that are stable and can be cost-effectively produced at large scale. Here, a biopolymer particle (BP) vaccine technology that can be quickly adapted to new and emerging variants of SARS-CoV-2 is used. Coronavirus antigen-coated BPs are described as vaccines against SARS-CoV-2. The spike protein subunit S1 or epitopes from S and M proteins (SM) plus/minus the nucleocapsid protein (N) are selected as antigens to either coat BPs during assembly inside engineered Escherichia coli or BPs are engineered to specifically ligate glycosylated spike protein (S1-ICC) produced by using baculovirus expression in insect cell culture (ICC). BP vaccines are safe and immunogenic in mice. BP vaccines, SM-BP-N and S1-ICC-BP induced protective immunity in the hamster SARS-CoV-2 infection model as shown by reduction of virus titers up to viral clearance in lungs post infection. The BP platform offers the possibility for rapid design and cost-effective large-scale manufacture of ambient temperature stable and globally available vaccines to combat the coronavirus disease 2019 (COVID-19) pandemic.

Recent Advances and Applications of Plant-Based Bioactive Saponins in Colloidal Multiphase Food Systems.

The naturally occurring saponins exhibit remarkable interfacial activity and also possess many biological activities linking to human health benefits, which make them particularly attractive as bifunctional building blocks for formulation of colloidal multiphase food systems. This review focuses on two commonly used food-grade saponins, Quillaja saponins (QS) and glycyrrhizic acid (GA), with the aim of clarifying the relationship between the structural features of saponin molecules and their subsequent self-assembly and interfacial properties. The recent applications of these two saponins in various colloidal multiphase systems, including liquid emulsions, gel emulsions, aqueous foams and complex emulsion foams, are then discussed. A particular emphasis is on the unique use of GA and GA nanofibrils as sole stabilizers for fabricating various multiphase food systems with many advanced qualities including simplicity, ultrastability, stimulability, structural viscoelasticity and processability. These natural saponin and saponin-based colloids are expected to be used as sustainable, plant-based ingredients for designing future foods, cosmetics and pharmaceuticals.

Antiviral Activity of Peptide-Based Assemblies.

The COVID-19 pandemic highlighted the importance of developing surfaces and coatings with antiviral activity. Here, we present, for the first time, peptide-based assemblies that can kill viruses. The minimal inhibitory concentration (MIC) of the assemblies is in the range tens of micrograms per milliliter. This value is 2 orders of magnitude smaller than the MIC of metal nanoparticles. When applied on a surface, by drop casting, the peptide spherical assemblies adhere to the surface and form an antiviral coating against both RNA- and DNA-based viruses including coronavirus. Our results show that the coating reduced the number of T4 bacteriophages (DNA-based virus) by 3 log, compared with an untreated surface and 6 log, when compared with a stock solution. Importantly, we showed that this coating completely inactivated canine coronavirus (RNA-based virus). This peptide-based coating can be useful wherever sterile surfaces are needed to reduce the risk of viral transmission.

Phase transitions in virology.

Viruses have established relationships with almost every other living organism on Earth and at all levels of biological organization: from other viruses up to entire ecosystems. In most cases, they peacefully coexist with their hosts, but in most relevant cases, they parasitize them and induce diseases and pandemics, such as the AIDS and the most recent avian influenza and COVID-19 pandemic events, causing a huge impact on health, society, and economy. Viruses play an essential role in shaping the eco-evolutionary dynamics of their hosts, and have been also involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organization, from the molecular mechanisms of genome replication, gene expression and encapsidation, to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as occurs with temperature separating phases in a liquid, define sharp qualitative types of behaviour. Thesephase transitionsare very well known in physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing us to better understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review well-known mathematical models of transition phenomena in virology. We suggest that the advantages of abstract, simplified pictures used in physics are also the key to properly understanding the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across scales and their evolutionary and clinical implications are outlined.

CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays.

CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction studies. We show that bespoke peptide libraries fused to catalytically inactive Cas9 (dCas9) and barcoded with unique single guide RNA (sgRNA) molecules self-assemble from a single mixed pool to programmable positions on a DNA microarray surface for rapid, multiplexed binding assays. We develop dCas9-displayed saturation mutagenesis libraries to characterize antibody-epitope binding for a commercial anti-FLAG monoclonal antibody and human serum antibodies. We also show that our platform can be used for viral epitope mapping and exhibits promise as a multiplexed diagnostics tool. Our CRISPR-based peptide display platform and the principles of complex library self-assembly using dCas9 could be adapted for rapid interrogation of varied customized protein libraries or biological materials assembly using DNA scaffolding.