SERS nanostructures with engineered active peptides against an immune checkpoint protein.

The immune checkpoint programmed death ligand 1 (PD-L1) protein is expressed by tumor cells and it suppresses the killer activity of CD8+ T-lymphocyte cells binding to the programmed death 1 (PD-1) protein of these immune cells. Binding to either PD-L1 or PD1 is used for avoiding the inactivation of CD8+ T-lymphocyte cells. We report, for the first time, Au plasmonic nanostructures with surface-enhanced Raman scattering (SERS) properties (SERS nanostructures) and functionalized with an engineered peptide (CLP002: Trp-His-Arg-Ser-Tyr-Tyr-Thr-Trp-Asn-Leu-Asn-Thr), which targets PD-L1. Molecular dynamics calculations are used to describe the interaction of the targeting peptide with PD-L1 in the region where the interaction with PD-1 occurs, showing also the poor targeting activity of a peptide with the same amino acids, but a scrambled sequence. The results are confirmed experimentally since a very good targeting activity is observed against the MDA-MB-231 breast adenocarcinoma cancer cell line, which overexpresses PD-L1. A good activity is observed, in particular, for SERS nanostructures where the CLP002-engineered peptide is linked to the nanostructure surface with a short charged amino acid sequence and a long PEG chain. The results show that the functionalized SERS nanostructures show very good targeting of the immune checkpoint PD-L1.

Investigation into the Influence of the Process Parameters on the Stability of a Poly(Vinyl)-Alcohol-Based Coating System.

Most tablets put on the market are coated with polymers soluble in water. The Opadry II 85 series from Colorcon Inc., is a family of PVA-based products marketed since the 1990s. Despite numerous publications on the properties of PVA, to date, limited work has been undertaken to determine the physico-chemical parameters (i.e., UV light, high temperature, and relative humidity) that could affect the performance of PVA-based coatings. To this end, we performed artificial ageing processes on samples made of Opadry Orange II or of some selected components of this coating and analysed them by means of a multidisciplinary approach, using, for example, FTIR, NMR, rheology, and DMTA measurements. In this way, we analysed the influence of the critical components of the Opadry Orange II formula, such as titanium dioxide and aluminium hydroxide, on the coating characteristics under ageing conditions.

A Spectroscopic and Molecular Dynamics Study on the Aggregation Properties of a Lipopeptide Analogue of Liraglutide, a Therapeutic Peptide against Diabetes Type 2.

The pharmacokinetics of peptide drugs are strongly affected by their aggregation properties and the morphology of the nanostructures they form in their native state as well as in their therapeutic formulation. In this contribution, we analyze the aggregation properties of a Liraglutide analogue (LG18), a leading drug against diabetes type 2. LG18 is a lipopeptide characterized by the functionalization of a lysine residue (K26) with an 18C lipid chain. To this end, spectroscopic experiments, dynamic light scattering measurements, and molecular dynamics simulations were carried out, following the evolution of the aggregation process from the small LG18 clusters formed at sub-micromolar concentrations to the mesoscopic aggregates formed by aged micromolar solutions. The critical aggregation concentration of LG18 in water (pH = 8) was found to amount to 4.3 µM, as assessed by the pyrene fluorescence assay. MD simulations showed that the LG18 nanostructures are formed by tetramer building blocks that, at longer times, self-assemble to form micrometric supramolecular architectures.

Ultrasound-Stimulated PVA Microbubbles as a Green and Handy Tool for the Cleaning of Cellulose-Based Materials.

One of the main issues in the cultural heritage field of restoration chemistry is the identification of greener and more effective methods for the wet cleaning of paper artefacts, which serve as witnesses to human history and custodians of cultural values. In this context, we propose a biocompatible method to perform wet cleaning on paper based on the use of 1 MHz ultrasound in combination with water-dispersed polyvinyl alcohol microbubbles (PVAMBs), followed by dabbing with PVA-based hydrogel. This method can be applied to both old and new papers. FTIR spectroscopy, X-ray diffraction, HPLC analysis, pH measurements and tensile tests were performed on paper samples, to assess the efficacy of the cleaning system. According to the results, ultrasound-activated PVAMB application allows for an efficient interaction with rough and porous cellulose paper profiles, promoting the removal of cellulose degradation byproducts, while the following hydrogel dabbing treatment guarantees the removal of cleaning materials residues. Moreover, the results also pointed out that after the treatment no thermal or mechanical damages had affected the paper. In conclusion, the readability of these kinds of artifacts can be improved without causing an alteration of their structural properties, while mitigating the risk of ink diffusion.

An Insight into the Degradation Processes of the Anti-Hypertensive Drug Furosemide.

Furosemide (FUR), an active pharmaceutical ingredient (API) belonging to a group of drugs known as loop diuretics, has widespread use, but, is characterized by a strong instability to light, which causes chemical transformations that could give a yellowing phenomenon and have a significant impact from a health and marketing point of view. Many studies have tried to explain this phenomenon under different experimental conditions, but no detailed explanation of the yellowing phenomenon has been provided. This work, unlike the others, provides an overall view and explanation of the behavior of FUR in relation to the yellowing phenomenon, both in the solution and in solid state, considering several aspects, such as light exposure, presence of oxygen, and moisture effects.

Inspection on the Mechanism of SARS-CoV-2 Inhibition by Penciclovir: A Molecular Dynamic Study.

In recent years, humanity has had to face a critical pandemic due to SARS-CoV-2. In the rapid search for effective drugs against this RNA-positive virus, the repurposing of already existing nucleotide/nucleoside analogs able to stop RNA replication by inhibiting the RNA-dependent RNA polymerase enzyme has been evaluated. In this process, a valid contribution has been the use of in silico experiments, which allow for a rapid evaluation of the possible effectiveness of the proposed drugs. Here we propose a molecular dynamic study to provide insight into the inhibition mechanism of Penciclovir, a nucleotide analog on the RNA-dependent RNA polymerase enzyme. Besides the presented results, in this article, for the first time, molecular dynamic simulations have been performed considering not only the RNA-dependent RNA polymerase protein, but also its cofactors (fundamental for RNA replication) and double-strand RNA.

Protection against proteolysis of a targeting peptide on gold nanostructures.

Cell targeting has been considered an important strategy in diagnostic and therapeutic applications. Among different targeting units, peptides have emerged for their ability to bind to many different cellular targets, their scarce immunogenicity and the possibility of introducing multiple copies on nanosystems, providing high avidity for the target. However, their sensitivity to proteases strongly limits their applications in vivo. Here, we show that when presented on the surface of nanostructures, peptide stability to proteolysis is strongly improved without reducing the targeting activity. We prepared plasmonic nanostructures functionalized with a dodecapeptide (GE11) which targets EGFR, a protein overexpressed on different types of tumors. Two types of nanosystems were prepared in which the targeting unit was either directly linked to gold nanoparticles or through a PEG chain, resulting in a different peptide density on the surface of nanostructures. The peptide was rapidly degraded in 20% human serum or in the presence of isolated serine proteases, whereas no significant proteolytic fragments were detected during incubation of the nanosystems and after 24 h digestion, the nanostructures maintained their targeting activity and selectivity on colon cancer cells. Molecular dynamic calculations of the interaction of the nanostructure with chymotrypsin suggest that the formation of the enzyme-peptide complex, the first step in the mechanism of peptide hydrolysis, is highly unlikely because of the constraint imposed by the link of the peptide to the nanoparticle. These results support the utilization of peptides as active targeting units in nanomedicine.

Ultrasound-Stimulated PVA Microbubbles for Adhesive Removal from Cellulose-Based Materials: A Groundbreaking Low-Impact Methodology.

In this work, we shed new light on ultrasound contrast agents applied to the field of cultural heritage as an invaluable fine-tune cleaning tool for paper artworks. In this context, one of the primary and challenging issues is the removal of modern adhesives from paper artifacts. Modern adhesives are synthetic polymers whose presence enhances paper degradation and worsens its optical features. A thorough analytical and high-spatial-resolution combined study was successfully performed to test the capability of poly(vinyl alcohol)-based microbubbles stimulated by a proper noninvasive 1 MHz ultrasound field exposure in removing these adhesives from paper surfaces, in the absence of volatile invasive and toxic chemicals and without damaging paper and/or leaving residues. We demonstrate that poly(vinyl alcohol)-shelled microbubbles are suitable for interacting with paper surfaces, targeting and boosting in a few minutes the nondamaging removal of adhesive particles from paper samples thanks to their peculiar shell composition together with their ultrasound dynamics.

From nanoaggregates to mesoscale ribbons: the multistep self-organization of amphiphilic peptides.

This paper reports atomic force microscopy results and molecular dynamics simulations of the striking differences of long-term self-organization structures of negatively charged (AcA4)2KD (double tail) and AcA4D (single tail) peptides, respectively, forming micrometer-long, linearly ordered ribbon-like structures and nanometer-sized, unstructured, round-shaped aggregates. The subsequent formation steps of the long-range nanoribbons, experimentally observed only for the "double tail" (AcA4)2KD peptide, are analyzed in detail, showing that the initial "primary" unstructured round-shaped aggregates progressively evolve into longer nanofilaments and into micrometer-long, network-forming nanoribbon moieties. In particular, the long-range self-organization of the "double tail" peptides appears to be closely related to electrostatically driven diffusional motions of the primary aggregates and nanofilaments. The diffusional freedom degrees are prompted by the formation of a dynamic ternary air/liquid/substrate interface, due to the water evaporation process from the ultrathin films of the peptide solution cast onto a solid mica substrate. Overall, the initial aggregation of unstructured round-shaped moieties, for both the peptides, can be seen as an entropy-driven process, involving the intra- and intermolecular interactions of hydrophobic parts of the peptides, while the further formation of long nanoribbons, only for "double tail" peptides, can be viewed in terms of an enthalpy-driven process, mainly due to the predominant electrostatic interactions between the charged heads of the interacting peptides. The role of the solid-liquid interface, as the locus of the enthalpy-driven linear organization, is also highlighted.

Coarse-Grained Simulation of the Adsorption of Water on Au(111) Surfaces Using a Modified Stillinger-Weber Potential.

For reproducing the behavior of water molecules adsorbed on gold surfaces in terms of density of both bulk and interfacial water and in terms of structuring of water on top of gold atoms, the implementation of a multibody potential is necessary, thus the Stillinger-Weber potential was tested. The goal is using a single nonbonded potential for coarse-grained models, without the usage of explicit charges. In order to modify the angular part of the Stillinger-Weber potential from a single cosine to a piecewise function accounting for multiple equilibrium angles, employed for Au-Au-Au and Au-Au-water triplets, it is necessary to create a version of the simulation package LAMMPS that supports the assignment of multiple favored angles. This novel approach is able to reproduce the data obtained using quantum mechanical calculations and density profiles of both bulk and adsorbed water molecules obtained using classical polarizable force fields.

Aggregation propensity of therapeutic fibrin-homing pentapeptides: insights from experiments and molecular dynamics simulations.

CREKA (Cys-Arg-Glu-Lys-Ala) and its engineered analogue CRMeEKA, in which Glu has been replaced by N-methyl-Glu to provide resistance against proteolysis, are emerging pentapeptides that were specifically designed to bind fibrin-fibronectin complexes accumulated in the walls of tumour vessels. However, many of the intrinsic properties of CREKA and CRMeEKA, which are probably responsible for their different behaviour when combined with other materials (such as polymers) for diagnosis and therapeutics, remain unknown yet. The intrinsic tendency of these pentapeptides to form aggregates has been analysed by combining experimental techniques and atomistic Molecular Dynamics (MD) simulations. Dynamic light scattering assays show the formation of nanoaggregates that increase in size with the peptide concentration, even though aggregation occurs sooner for CRMeEKA, independently of the peptide concentration. FTIR and circular dichroism spectroscopy studies suggest that aggregated pentapeptides do not adopt any secondary structure. Atomistic MD trajectories show that CREKA aggregates faster and forms bigger molecular clusters than CRMeEKA. This behaviour has been explained by stability of the conformations adopted by un-associated peptide strands. While CREKA molecules organize by forming intramolecular backbone - side chain hydrogen bonds, CRMeEKA peptides display main chain - main chain hydrogen bonds closing very stable γ- or ß-turns. Besides, energetic analyses reveal that CRMeEKA strands are better solvated in water than CREKA ones, independent of whether they are assembled or un-associated.

Polyvinyl alcohol based hydrogels as new tunable materials for application in the cultural heritage field.

Hydrogel-based cleaning of paper artworks is an increasingly widespread process in the cultural heritage field. However, the search for tuned (compatible, highly retentive and not perishable) hydrogels is a challenging open question. In this paper, a complete characterization of chemical hydrogels based on polyvinyl alcohol (PVA) crosslinked with telechelic PVA and their remarkable performances as gels for cleaning paper artworks are reported. The rheological properties, porosity, water content of these gels were determined and analyzed as a function of the components concentration during synthesis. Due mechanical and retentive properties, the reported gels are optimum candidates for paper cleaning applications. The efficacy of these PVA-based gels has been demonstrated applying them on the surface of the sheets of several paper artworks, and characterizing the samples before and after the cleaning process by means of a multidisciplinary approach involving spectroscopic and chromatographic tests.

Rational Design of Antiangiogenic Helical Oligopeptides Targeting the Vascular Endothelial Growth Factor Receptors.

Tumor angiogenesis, essential for cancer development, is regulated mainly by vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs), which are overexpressed in cancer cells. Therefore, the VEGF/VEGFR interaction represents a promising pharmaceutical target to fight cancer progression. The VEGF surface interacting with VEGFRs comprises a short α-helix. In this work, helical oligopeptides mimicking the VEGF-C helix were rationally designed based on structural analyses and computational studies. The helical conformation was stabilized by optimizing intramolecular interactions and by introducing helix-inducing Cα,α-disubstituted amino acids. The conformational features of the synthetic peptides were characterized by circular dichroism and nuclear magnetic resonance, and their receptor binding properties and antiangiogenic activity were determined. The best hits exhibited antiangiogenic activity in vitro at nanomolar concentrations and were resistant to proteolytic degradation.

Molecular Sponge: pH-Driven Reversible Squeezing of Stimuli-Sensitive Peptide Monolayers.

The cyclic change of structure, thickness, and density, with pH switching from acidic (pH = 3) to basic (pH = 11) condition, has been revealed for chemisorbed monolayers of the peptide Lipo-Aib-Lys-Leu-Aib-Lys-Lys-Leu-Aib-Lys-Ile-Lol, a trichogin GA IV-analogue carrying Lys residues instead of Gly ones at positions 2, 5, 6, and 9, while a homologous peptide not containing Lys residues does not show any response to pH changes. Experimental and theoretical results, obtained by means of quartz crystal microbalance with dissipation monitoring, surface plasmon resonance, nanoplasmonic sensing technique, Fourier transform infrared-reflection attenuated spectroscopy and dynamic force spectroscopy, and molecular dynamics simulations provide detailed information on the overall monolayer structure changes with pH, including the analysis of the intra- and interchain peptide dynamics, the structure of the peptide layer/water/solid interface, as well as the position and role of solvation and nonsolvation water. The observed stimuli-responsive behavior of L1 peptide monolayers is accounted in terms of the occurrence of a pH-induced wetting/dewetting process, due to the pH-induced switching of the hydrophilic character of charged lysine groups to hydrophobic one of the same uncharged groups, along the peptide chain. This behavior in turn promotes the collective change of the aggregation state of the peptide chains. The present results may pave the way to critically reexamine the mechanism of stimuli-responsive systems.

Controlling the Formation of Peptide Films: Fully Developed Helical Peptides are Required to Obtain a Homogenous Coating over a Large Area.

The influence of conformational dynamics on the self-assembly process of a conformationally constrained analogue of the natural antimicrobial peptide Trichogin GA IV was analysed by spectroscopic methods, microscopy imaging at nanometre resolution, and molecular dynamics simulations. The formation of peptide films at the air/water interface and their deposition on a graphite or a mica substrate were investigated. A combination of experimental evidence with molecular dynamics simulation was used to demonstrate that only the fully developed helical structure of the analogue promotes formation of ordered aggregates that nucleate the growth of micrometric rods, which give rise to homogenous coating over wide regions of the hydrophilic mica. This work proves the influence of helix flexibility on peptide self-organization and orientation on surfaces, key steps in the design of bioinspired organic/inorganic hybrid materials.

Understanding the good and poor cell targeting activity of gold nanostructures functionalized with molecular units for the epidermal growth factor receptor.

Nanostructures can strongly interact with cells or other biological structures; furthermore when they are functionalized with targeting units, they are of great interest for a variety of applications in the biotechnology field like those for efficient imaging, diagnosis and therapy and in particular for cancer theranostics. Obtaining targeting with good specificity and sensitivity is a key necessity, which, however, is affected by the complexity of the interactions between the nanostructures and the biological components. In this work we report the study of specificity and sensitivity of gold nanoparticles functionalized with the peptide GE11 for the targeting of the epidermal growth factor receptor, expressed on many cells and, in particular, on many types of cancer cells. We show how a combination of spectroscopic measurements and molecular dynamics simulations allows the comprehension of the targeting activity of peptides linked to the surface of gold nanostructures and how the targeting is tuned by the presence of polyethylene glycol chains.

Tuning the Morphology of Nanostructured Peptide Films by the Introduction of a Secondary Structure Conformational Constraint: A Case Study of Hierarchical Self-Assembly.

Peptide self-assembly is ubiquitous in nature. It governs the organization of proteins, controlling their folding kinetics and preserving their structural stability and bioactivity. In this connection, model oligopeptides may give important insights into the molecular mechanisms and elementary forces driving the formation of supramolecular structures. In this contribution, we show that a single residue substitution, that is, Aib (α-aminoisobutyric acid) in place of Ala at position 4 of an -(l-Ala)5-homo-oligomer, strongly alters the aggregation process. In particular, this process is initiated by the formation of small peptide clusters that promote aggregation on the nanometer scale and, through a hierarchical self-assembly, lead to mesoscopic structures of micrometric dimensions. Furthermore, we show that the use of the well-established Langmuir-Blodgett technique represents an effective strategy for coating extended areas of inorganic substrates by densely packed peptide layers, thus paving the way for application of peptide films as templates for biomineralization, biocompatible coating of surfaces, and scaffolds for tissue engineering.

Orienting proteins by nanostructured surfaces: evidence of a curvature-driven geometrical resonance.

Experimental and theoretical reports have shown that nanostructured surfaces have a dramatic effect on the amount of protein adsorbed and the conformational state and, in turn, on the performances of the related devices in tissue engineering strategies. Here we report an innovative method to prepare silica-based nanostructured surfaces with a reproducible, well-defined local curvature, consisting of ordered hexagonally packed arrays of curved hemispheres, from nanoparticles of different diameters (respectively 147 nm, 235 nm and 403 nm). The nanostructured surfaces have been made chemically homogeneous by partially embedding silica nanoparticles in poly(hydroxymethylsiloxane) films, further modified by means of UV-O3 treatments. This paper has been focused on the experimental and theoretical study of laminin, taken as a model protein, to study the nanocurvature effects on the protein configuration at nanostructured surfaces. A simple model, based on the interplay of electrostatic interactions between the charged terminal domains of laminin and the nanocurved charged surfaces, closely reproduces the experimental findings. In particular, the model suggests that nanocurvature drives the orientation of rigid proteins by means of a "geometrical resonance" effect, involving the matching of dimensions, charge distribution and spatial arrangement of both adsorbed molecules and adsorbent nanostructures. Overall, the results pave the way to unravel the nanostructured surface effects on the intra- and inter-molecular organization processes of proteins.

Enhanced EGFR Targeting Activity of Plasmonic Nanostructures with Engineered GE11 Peptide.

Plasmonic nanostructures show important properties for biotechnological applications, but they have to be guided on the target for exploiting their potentialities. Antibodies are the natural molecules for targeting. However, their possible adverse immunogenic activity and their cost have suggested finding other valid substitutes. Small molecules like peptides can be an alternative source of targeting agents, even if, as single molecules, their binding affinity is usually not very good. GE11 is a small dodecapeptide with specific binding to the epidermal growth factor receptor (EGFR) and low immunogenicity. The present work shows that thousands of polyethylene glycol (PEG) chains modified with lysines and functionalized with GE11 on clusters of naked gold nanoparticles, obtained by laser ablation in water, achieves a better targeting activity than that recorded with nanoparticles decorated with the specific anti-EGFR antibody Cetuximab (C225). The insertion of the cationic spacer between the polymeric part of the ligand and the targeting peptide allows for a proper presentation of GE11 on the surface of the nanosystems. Surface enhanced resonance Raman scattering signals of the plasmonic gold nanoparticles are used for quantifying the targeting activity. Molecular dynamic calculations suggest that subtle differences in the exposition of the peptide on the PEG sea are important for the targeting activity.

Molecular Dynamics Simulations of the Host Defense Peptide Temporin L and Its Q3K Derivative: An Atomic Level View from Aggregation in Water to Bilayer Perturbation.

Temporin L (TempL) is a 13 residue Host Defense Peptide (HDP) isolated from the skin of frogs. It has a strong affinity for lipopolysaccharides (LPS), which is related to its high activity against Gram-negative bacteria and also to its strong tendency to neutralize the pro-inflammatory response caused by LPS release from inactivated bacteria. A designed analog with the Q3K substitution shows an enhancement in both these activities. In the present paper, Molecular Dynamics (MD) simulations have been used to investigate the origin of these improved properties. To this end, we have studied the behavior of the peptides both in water solution and in the presence of LPS lipid-A bilayers, demonstrating that the main effect through which the Q3K substitution improves the peptide activities is the destabilization of peptide aggregates in water.