Adaptable Self-Assembly of a PEG Dendrimer-Coiled Coil Conjugate.

Self-assembly of designed molecules has enabled the construction of a variety of functional nanostructures. Specifically, adaptable self-assembly has demonstrated several advantageous features for smart materials. Here, we demonstrate that an α-helical coiled coil conjugated with a dendrimer can adapt to spatial restriction due to the strong steric repulsion between dendrimer chains. The adaptable transformation of a tetrameric coiled coil to a trimeric coiled coil can be confirmed using analytical ultracentrifugation upon conjugation of the dendrimer to the coiled coil-forming building block. Interestingly, circular dichroism spectroscopy analysis of the dendrimer conjugate revealed an unconventional trend: the multimerization of the coiled coil is inversely dependent on concentration. This result implies that the spatial crowding between the bulky dendritic chains is significantly stronger than that between linear chains, thereby affecting the overall assembly process. We further illustrated the application potential by decorating the surface of gold nanorods (AuNRs) with the adaptable coiled coil. The dendrimer-coiled coil peptide conjugate can be utilized to fabricate organic-inorganic nanohybrids with enhanced colloidal and thermal stabilities. This study demonstrates that the coiled coil can engage in the adaptable mode of self-assembly with the potential to form dynamic peptide-based materials.

Inhibition of protein-protein interactions using biodegradable depsipeptide nanoassemblies.

Although peptides notoriously have poor intrinsic pharmacokinetic properties, it is well-known that nanostructures with excellent pharmacokinetic properties can be designed. Noticing that peptide inhibitors are generally nonpolar, here, we consolidate the peptide inhibitor targeting intracellular protein-protein interactions (PPIs) as an integral part of biodegradable self-assembled depsipeptide nanostructures (SdPNs). Because the peptide inhibitor has the dual role of PPI inhibition and self-assembly in this design, problems associated with the poor pharmacokinetics of peptides and encapsulation/entrapment processes can be overcome. Optimized SdPNs displayed better tumor targeting and PPI inhibition properties than the comparable small molecule inhibitor in vivo. Kinetics of PPI inhibition for SdPNs were gradual and controllable in contrast to the rapid inhibition kinetics of the small molecule. Because SdPN is modular, any appropriate peptide inhibitor can be incorporated into the platform without concern for the poor pharmacokinetic properties of the peptide.

Self-Assembled Protein Nanostructures via Irreversible Peptide Assembly.

The quaternary structure of proteins extends the functionality of monomeric proteins. Similarly, self-assembled protein nanostructures (SPrNs) have great potential to improve the functionality and complexity of proteins; however, the difficulty associated with the fabrication of SPrNs is far greater than that associated with the fabrication of self-assembled peptides or polymers and often requires sophisticated computational design. To make the process of SPrN formation simpler and more intuitive, herein, we devise a strategy to adopt an irreversible self-assembled peptide nanostructure (SPeN) process en route to the formation of SPrNs. The strategy employs three sequential steps: first, the formation of SPeNs (an equilibrium process); second, covalent capture of SPeNs (an irreversible process); third, the final assembly of SPrNs via protein-peptide interactions (an equilibrium process). This strategy allowed us to fabricate SPrNs in which the size of the protein was approximately 9 times higher than that of the self-assembling peptide. Furthermore, we demonstrated that the irreversible SPeN could be used as a primary building block for assembly into superstructures. Overall, this strategy is conceptually as simple as SPeN fabrication and is potentially applicable to any soluble protein.

Modulating the folding and binding of peptides using a stimuli-responsive molecular tweezer.

This study presents the development of a ß-hairpin (tryptophan zipper, Trpzip)-based molecular tweezer (MT) that can control the folding and binding of α-helical peptides. When an α-helix isolated from the p53 protein was conjugated with Trpzip in an optimized macrocyclic structure, the folded ß-hairpin stabilized the helix conformation through the side chain-to-side chain stapling strategy, which notably enhanced target (hDM2) affinity of the peptide. On the other hand, the helicity and binding affinity were significantly reduced when the hairpin was unfolded by a redox stimulus. This stimulus-responsive property was translated into the effective capture and release of model multivalent biomaterials, hDM2-gold nanoparticle conjugates. Since numerous protein interactions are mediated by α-helical peptides, these results suggest that the ß-hairpin-based MT holds great potential to be utilized in various biomedical applications, such as protein interaction inhibition and cancer biomarker (e.g., circulating tumor cells and exosomes) detection.

Cooperative Assembly of Self-Adjusting α-Helical Coiled Coils along the Length of an mRNA Chain to Form a Thermodynamically Stable Nanotube Carrier.

Although mRNA delivery technology is very promising, problems in safety and transport arise due to the intrinsically low thermodynamic stability of the current mRNA carriers. Considering that mRNAs are filamentous and a nanotube is one of the most thermodynamically stable shapes among nanoassemblies, a nanotube is one of the most stable supramolecular structures that can be assembled with mRNA. Here, we develop a nanotube-shaped filamentous mRNA delivery platform that shows exceptionally high thermodynamic stability. The key to the development of the mRNA nanotube is the design of self-adjusting supramolecular building blocks (SABs) that have two disparate properties, i.e., dynamic property and stiffness, in a single molecule. The counterbalance of the dynamic property and stiffness in SABs enables the coating of mRNA by winding its way through the flexible and irregular mRNA chain via cooperative interactions. SAB nanotubes with targeting ligands installed show a high uptake efficiency in mammalian cells and controllable gene expression behavior. Thus, the mRNA nanotube provides an enabling technology toward the development of safe and stable mRNA vaccines and therapeutics.

Magnetic control of self-assembly and disassembly in organic materials.

Because organic molecules and materials are generally insensitive or weakly sensitive to magnetic fields, a certain means to enhance their magnetic responsiveness needs to be exploited. Here we show a strategy to amplify the magnetic responsiveness of self-assembled peptide nanostructures by synergistically combining the concepts of perfect α-helix and rod-coil supramolecular building blocks. Firstly, we develop a monomeric, nonpolar, and perfect α-helix (MNP-helix). Then, we employ the MNP-helix as the rod block of rod-coil amphiphiles (rod-coils) because rod-coils are well-suited for fabricating responsive assemblies. We show that the self-assembly processes of the designed rod-coils and disassembly of rod-coil/DNA complexes can be controlled in a magnetically responsive manner using the relatively weak magnetic field provided by the ordinary neodymium magnet [0.07 ~ 0.25 Tesla (T)]. These results demonstrate that magnetically responsive organic assemblies usable under practical conditions can be realized by using rod-coil supramolecular building blocks containing constructively organized diamagnetic moieties.

Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets.

Although interest in stabilized α-helical peptides as next-generation therapeutics for modulating biomolecular interfaces is increasing, peptides have limited functionality and stability due to their small size. In comparison, α-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated α-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain α-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The α-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized α-helix pharmaceuticals.

Structural control of self-assembled peptide nanostructures to develop peptide vesicles for photodynamic therapy of cancer.

Vesicles such as liposomes, polymersomes, and exosomes have been widely used as drug delivery carriers; however, peptide vesicles (peptidesomes) despite their potential utility are far less well developed. Peptidesomes are distinctive because peptides play dual roles as a self-assembly building block and a bioactive functional unit. In order for peptidesomes to become successful nanodrugs, the issues related to differences in nanostructural properties between in vitro and in vivo conditions should be addressed. Here, we delineate a multivariate approach to feedback control the structures of peptide building blocks, nanoparticle size, drug loading process, nanoparticle aggregation, cytotoxicity, cell targeting capability, endosome disruption function, protease resistance, and in vivo performance, which eventually enabled the successful development of a highly efficacious peptidesome for in vivo cancer therapy. This study lays the groundwork for the successful in vivo translation of peptide nanodrugs.

In pursuit of next-generation therapeutics: Antimicrobial peptides against superbugs, their sources, mechanism of action, nanotechnology-based delivery, and clinical applications.

Antimicrobial peptides (AMPs) attracted attention as potential source of novel antimicrobials. Multi-drug resistant (MDR) infections have emerged as a global threat to public health in recent years. Furthermore, due to rapid emergence of new diseases, there is pressing need for development of efficient antimicrobials. AMPs are essential part of the innate immunity in most living organisms, acting as the primary line of defense against foreign invasions. AMPs kill a wide range of microorganisms by primarily targeting cell membranes or intracellular components through a variety of ways. AMPs can be broadly categorized based on their physico-chemical properties, structure, function, target and source of origin. The synthetic analogues produced either with suitable chemical modifications or with the use of suitable delivery systems are projected to eliminate the constraints of toxicity and poor stability commonly linked with natural AMPs. The concept of peptidomimetics is gaining ground around the world nowadays. Among the delivery systems, nanoparticles are emerging as potential delivery tools for AMPs, amplifying their utility against a variety of pathogens. In the present review, the broad classification of various AMPs, their mechanism of action (MOA), challenges associated with AMPs, current applications, and novel strategies to overcome the limitations have been discussed.

Unique behaviour of the α-helix in bending deformation.

The maximum degree of bending that can be tolerated by the rigid rod-like α-helix remains unknown; however, it should be very difficult or even impossible to make α-helices with varying degrees of curvature in folded proteins. As an experimentally tractable model, here we utilize cyclic proteins and peptides to determine the maximum possible bending in the α-helix. We artificially enforced bending in the α-helices by using variously sized macrocycles and compared the structural characteristics of the macrocycles with those of their linear counterparts. This differential analysis reveals that the radius of curvature (RC) for the maximally bent α-helix is approximately 10 times smaller than those of typical α-helices found in natural proteins. Together with the novel finding of the limit of α-helix deformation, excessively bent α-helices can be further utilized in designing de novo peptides and proteins with unique structures and peculiar functions.

Age and Gender Effects on Genotoxicity in Diesel Exhaust Particles Exposed C57BL/6 Mice.

There is growing evidence that the accumulation of DNA damage induced by fine particulate matter (PM2.5) exposure is an underlying mechanism of pulmonary disease onset and progression. However, there is a lack of experimental evidence on whether common factors (age, gender) affect PM2.5 induced genomic damage. Here, we assessed the DNA damage potency of PM2.5 using conventional genotoxicity testing in old male and female mice aged 8 and 40 weeks. Mice were intratracheally instilled with diesel exhaust PM2.5 (DEP, NIST SRM 1650b), twice a week for 4 weeks. Exposure to DEP was not associated with an increase in the frequency of micronucleated polychromatic erythrocytes and did not induce a systemic genotoxic effect in the bone marrow. Meanwhile, the results from the comet assay showed a significant increase in DNA damage in DEP exposed mouse lung specimens. The positive relationship between DEP exposure and DNA damage is stronger in the older than in the younger group. Statistical analysis showed that there was a modifying effect of age on the association between PM2.5 exposure and DNA damage. Our results suggest that the age factor should be considered to better understand the cellular adverse effects of PM2.5.

Determination of Genotoxicity Attributed to Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line.

Several epidemiological studies concluded that inhalation of diesel exhaust particles (DEP) is associated with an increase in the relative risk of lung cancer. In vitro research evaluating the genetic damage and/or changes in gene expression have been attempted to explain the relationship between DEP exposure and carcinogenicity. However, to date, investigations have been largely confined to studies in immortalized or tumorigenic epithelial cell models. Few studies have investigated damage at the chromosomal level to DEP exposure in normal cell lines. Here, we present the genotoxic effects of DEP in normal cells (embryonic human lung fibroblasts) by conventional genotoxicity testing (micronuclei (MN) and comet assay). We show the differentially expressed genes and enriched pathways in DEP-exposed WI-38 cells using RNA sequencing data. We observed a significant increase in single-strand DNA breaks and the frequency of MN in DEP-exposed cells in a dose-dependent manner. The differentially expressed genes following DEP exposure were significantly enriched in the pathway for responding to xenobiotics and DNA damage. Taken together, these results show that DEP exposure induced DNA damage at the chromosomal level in normal human lung cells and provide information on the expression of genes associated with genotoxic stress.

Disaggregation of Amyloid-ß Plaques by a Local Electric Field Generated by a Vertical Nanowire Electrode Array.

The aggregation and accumulation of amyloid-ß (Aß) peptides is a characteristic pathology for Alzheimer's disease (AD). Although noninvasive therapies involving stimulation by electric field (EF) have been reported, the efficiency of Aß disaggregation needs to be further improved for this strategy to be used in clinical settings. In this study, we show that an electrode based on a vertical nanowire electrode array (VNEA) is far more superior to a typical flat-type electrode in disaggregating Aß plaques. The enhanced disaggregation efficiency of VNEA is due to the formation of high-strength local EF between the nanowires, as verified by in silico and empirical evidence. Compared with those of the flat electrode, the simulation data revealed that 19.8-fold and 8.8-fold higher EFs are generated above and between the nanowires, respectively. Moreover, empirical cyclic voltammetry data demonstrated that VNEA had a 2.7-fold higher charge capacity than the flat electrode; this is associated with the higher surface area of VNEA. The conformational transition of Aß peptides between the ß-sheet and α-helix could be sensitively monitored in real time by the newly designed in situ circular dichroism instrument. This highly efficient EF-configuration of VNEA will lower the stimulation power for disaggregating the Aß plaques, compared to that of other existing field-mediated modulation systems. Considering the complementary metal-oxide-semiconductor-compatibility and biocompatible strength of the EF for perturbing the Aß aggregation, our study could pave the way for the potential use of electric stimulation devices for in vivo therapeutic application as well as scientific studies for AD.

A Three-Dimensional Sensor to Recognize Amyloid-ß in Blood Plasma of Patients.

Detecting amyloid beta (Aß) in unpurified blood to diagnose Alzheimer's disease (AD) is challenging owing to low concentrations of Aß and the presence of many other substances in the blood. Here, we propose a 3D sensor for AD diagnosis using blood plasma, with pairs of 3D silicon micropillar electrodes with a comprehensive circuit configuration. The sensor is developed with synthesized artificial peptide and impedance analysis based on a maximum signal-to-noise ratio. Its sensitivity and selectivity were verified using an in vitro test based on samples of human blood serum, which showed its feasibility for application in diagnosis of AD by testing blood plasma of the AD patient. The 3D sensor is designed to improve reliability by checking the impedance of each pair multiple times via constructing a reference pair and a working pair on the same sensor. Therefore, we demonstrate the ability of the 3D sensor to recognize cases of AD using blood plasma and introduce its potential as a self-health care sensor for AD patients.

A Dodecapeptide Selected by Phage Display as a Potential Theranostic Probe for Colon Cancers.

AIM: Colon cancer is one of the leading causes of cancer-related mortality. However, specific biomarkers for its diagnosis or treatment are not established well. METHODS: We developed a colon-cancer specific peptide probe using phage display libraries. We validated the specificity of this probe to colon cancer cells with immunohistochemical staining and FACS analysis using one normal cell and five colon cancer cell lines. RESULTS: This peptide probe maintained binding affinity even after serum incubation. For therapeutic applications, this peptide probe was conjugated to hematoporphyrin, a photosensitizer, which showed a significantly enhanced cellular uptake and high photodynamic effect to kill tumor cells. As another application, we made a nanoparticle modified from the peptide probe. It efficiently delivered SN-38, an anticancer drug, into tumor cells, and its tumor-targeting ability was observed in vivo after intravenous injection to the same xenograft model. CONCLUSION: The noble dodecapeptide probe can be a promising candidate for both colon tumor diagnosis and targeted drug delivery.

Slow-Motion Self-Assembly: Access to Intermediates with Heterochiral Peptides to Gain Control over Alignment Media Development.

Understanding the intermediates or transition states in organic reactions has made it possible to develop theories and to synthesize important compounds. In contrast to organic reaction intermediates and even protein folding intermediates, the intermediates of peptide/protein self-assembly are not very well understood. Here we report that the self-assembly kinetics of linear heterochiral peptides are significantly slower than those of the corresponding homochiral peptides, which enables direct microscopic observation of assembly intermediates. By designing racemic or asymmetric heterochiral peptides, we were able to discover unusual mixed helical (MP-helix) and overtwisted intermediates. The convergence of equilibrium morphology between the homochiral and heterochiral peptides enables us to reasonably deduce the unobservable intermediates of rapidly assembling homochiral peptides. By utilizing the discovered information about the assembly intermediates, we were able to develop a functional NMR alignment medium that enables the measurement of residual dipolar couplings (RDCs) in a time-dependent manner. Although much less studied than their cyclic counterparts, the linear form of heterochiral peptides provides a means of obtaining a more in-depth understanding of the self-assembly pathway and of developing sophisticated bottom-up materials.

Self-Assembling Peptides and Their Application in the Treatment of Diseases.

Self-assembling peptides are biomedical materials with unique structures that are formed in response to various environmental conditions. Governed by their physicochemical characteristics, the peptides can form a variety of structures with greater reactivity than conventional non-biological materials. The structural divergence of self-assembling peptides allows for various functional possibilities; when assembled, they can be used as scaffolds for cell and tissue regeneration, and vehicles for drug delivery, conferring controlled release, stability, and targeting, and avoiding side effects of drugs. These peptides can also be used as drugs themselves. In this review, we describe the basic structure and characteristics of self-assembling peptides and the various factors that affect the formation of peptide-based structures. We also summarize the applications of self-assembling peptides in the treatment of various diseases, including cancer. Furthermore, the in-cell self-assembly of peptides, termed reverse self-assembly, is discussed as a novel paradigm for self-assembling peptide-based nanovehicles and nanomedicines.

A CMOS VEGF Sensor for Cancer Diagnosis Using a Peptide Aptamer-Based Functionalized Microneedle.

This paper presents the first CMOS Vascular Endothelial Growth Factor (VEGF) sensor for cancer diagnosis directly from human blood. The sensor incorporates a peptide aptamer-based microneedle that allows the detection of electrochemical reactions with VEGF. This results in a capacitance change between the microneedles and then reads out by a two-step capacitance-to-digital converter (CDC). The proposed two-step CDC consists of a coarse 5b slope ADC and a fine 14b continuous-time delta-sigma modulator (CTDSM). During slow peptide-binding, the slope ADC performs a coarse conversion and the results are used to adjust the current level of the stimulator. After settling of the peptide-binding, based on an adjusted stimulation current, the CTDSM measures the small capacitance changes of the sensor. The prototype chip is fabricated in a 65-nm CMOS process, occupying a 0.87 mm 2 active area. The power consumption is 270 muW. Thanks to the two-step approach, this work achieves a wide dynamic range of 18.3b, covering a large sensor-to-sensor variation. It also achieves a peak resolution of 13.7b, while maintaining errors in 1 to 100 nF baseline capacitance. The overall sensor system successfully detects the VEGF in both phosphate-buffered saline (PBS) and human blood serum. Without the use of precision instruments, this work achieves a resolution of 15 fM [Formula: see text] in range of 0.1 to 1000 pM and denotes the clear VEGF selectivity at 40× in PBS and 5× in the blood serum compared to other proteins (IgG, Con A, and cholera toxin).

Investigation of the Hydration State of Self-Assembled Peptide Nanostructures with Advanced Electron Paramagnetic Resonance Spectroscopy.

Probing the intermolecular interactions and local environments of self-assembled peptide nanostructures (SPNs) is crucial for a better understanding of the underlying molecular details of self-assembling phenomena. In particular, investigation of the hydration state is important to understand the nanoscale structural and functional characteristics of SPNs. In this report, we examined the local hydration environments of SPNs in detail to understand the driving force of the discrete geometric structural self-assembling phenomena for peptide nanostructures. Advanced electron paramagnetic resonance spectroscopy was used to probe the hydrogen bond formation and geometry as well as the hydrophobicity of the local environments at various spin-labeled sites in SPNs. The experimental results supplement the sparse experimental data regarding local structures of SPNs, such as the hydrogen bonding and the hydrophobicity of the local environment, providing important information on the formation of SPNs, which have immense potential for bioactive materials.

Real-Time Detection of Markers in Blood.

The real-time selective detection of disease-related markers in blood using biosensors has great potential for use in the early diagnosis of diseases and infections. However, this potential has not been realized thus far due to difficulties in interfacing the sensor with blood and achieving transparent circuits that are essential for detecting of target markers (e.g., protein, ions, etc.) in a complex blood environment. Herein, we demonstrate the real-time detection of a specific protein and ion in blood without a skin incision. Complementary metal-oxide-semiconductor technology was used to fabricate silicon micropillar array (SiMPA) electrodes with a height greater than 600 µm, and the surface of the SiMPA electrodes was functionalized with a self-assembling artificial peptide (SAP) as a receptor for target markers in blood, i.e., cholera toxin (CTX) and mercury(II) ions (Hg). The detection of CTX was investigated in both in vitro (phosphate-buffered saline and human blood serum, HBO model) and in vivo (mouse model) modes via impedance analysis. In the in vivo mode, the SiMPA pierces the skin, comes into contact with the blood system, and creates comprehensive circuits that include all the elements such as electrodes, blood, and receptors. The SiMPA achieves electrically transparent circuits and, thus, can selectively detect CTX in the blood in real time with a high sensitivity of 50 pM and 5 nM in the in vitro and in vivo modes, respectively. Mercury(II) ions can also be detected in both the in vitro and the in vivo modes by changing the SAP. The results illustrate that a robust sensor that can detect a variety of molecular species in the blood system in real time that will be helpful for the early diagnosis of disease and infections.