Physicochemical properties of SARS-CoV-2 for drug targeting,virus inactivation and attenuation,vaccine formulation and quality control

The material properties of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its proteins are discussed. We review the viral structure, size, rigidity, lipophilicity, isoelectric point, buoyant density and centrifugation conditions, stability against pH, temperature, UV light, gamma radiation, and susceptibility to various chemical agents including solvents and detergents. Possible inactivation, downstream, and formulation conditions are given including suitable buffers and some first ideas for quality-control methods. This information supports vaccine development and discussion with competent authorities during vaccine approval and is certainly related to drug-targeting strategies and hygienics. Several instructive tables are given, including the pI and grand average of hydropathicity (GRAVY) of SARS-CoV-1 and -2 proteins in comparison. SARS-CoV-1 and SARS-CoV-2 are similar in many regards, so information can often be derived. Both are unusually stable, but sensitive at their lipophilic membranes. However, since seemingly small differences can have strong effects, for example, on immunologically relevant epitope settings, unevaluated knowledge transfer from SARS-CoV-1 to SARS-CoV-2 cannot be advised. Published knowledge regarding downstream processes, formulations and quality assuring methods is, as yet, limited. However, standard approaches employed for other viruses and vaccines seem to be feasible including virus inactivation, centrifugation conditions, and the use of adjuvants.     

Current knowledge on the extraction,purification, identification,and validation of bioactive peptides from seaweed

Seaweed (macroalgae) is considered as a sustainable bioresource rich in high-quality nutrients such as protein. Seaweed protein can be used as an alternative to other protein sources. Furthermore, these proteins are natural reservoirs of bioactive peptides (BAPs) associated with various health benefits such as antioxidant, antihypertensive, and antidiabetic activities. However, seaweed-derived BAPs remain underexploited due to challenges that arise during protein extraction from algal biomass. Coupled with this, limited proteomic information exists regarding certain seaweed species. This review highlights the current state of the art of seaweed protein extraction techniques, e.g., liquid, ultrasound, microwave, pulsed electric field, and high hydrostatic pressure assisted extraction. The review also focuses on the enzymatic hydrolysis of seaweed proteins and characterization of the resultant hydrolysates/peptides using electrophoretic and chromatographic techniques. This includes reference to methods employed for separation, fractionation, and purification of seaweed BAPs, as well as the methodologies used for identification, e.g., analysis by mass spectrometry. Furthermore, a bioinformatics or in silico approach to aid discovery of seaweed BAPs is discussed herein. Based on the information available to date, it is suggested that further research is required in this area for the development of seaweed BAPs for nutraceutical applications.     

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins

Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. © 2019 Wiley Periodicals, Inc.     

Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers

The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz–Singh–Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.     

Third-Generation Solar Cells: Toxicity and Risk of Exposure

Solar energy is considered clean energy, and its use is predicted to increase in the near future. Most installed units today are crystalline solar cells, but the field is in constant development, and when the first dye sensitized solar cell was published by Grätzel and O'Reagan a new, third-generation, solar power was born. Highly toxic metals are used to produce the photovoltaic units today, and with the predicted increase in solar cell installation, the human health hazards of these panels could become an issue. Additionally, many of these materials are used in their nanoform, which is associated with an additional risk. In this article, we discuss the technology behind the third-generation solar cells with its valuable use of nanotechnology as well as the possible health hazard when such nanomaterials are used in solar power units. We will show that the main exposure will occur either during the development and production phases or at the end-of-life stage of the solar cells, where toxic material can leach into landfills, and subsequently into the environment and impact the ecosystem directly, or humans indirectly through edible plants or drinking water.     

Photodynamic Activity on Biofilm in Endotracheal Tubes of Patients Admitted to an Intensive Care Unit

Ventilator-associated pneumonia (VAP) is an infection that arises after endotracheal intubation affecting patients under intensive care. The presence of the endotracheal tube (ETT) is a risk factor since it is colonized by multispecies biofilm. Antimicrobial photodynamic therapy (aPDT) could be a strategy to decontaminate ETTs. We verify if methylene blue (MB) associated with external illumination of the ETT could be an alternative to destroy biofilm. We performed an in vitro and ex vivo study. In vitro study was performed with P. aeruginosa biofilm grew over ETT for 7 days. After treatment, the surviving cells were cultured for 3 days and the biofilm was analyzed by crystal violet absorbance. Ex vivo study employed ETT obtained from extubated patients. aPDT was performed with MB (100 µm ) and red LED (λ = 640±20 nm). We quantified the biofilm thickness and used scanning electron microscopy and fluorescence technique to verify morphological and functional changes after aPDT. Our results showed that bacteria remain susceptible to aPDT after sequential treatments. We also attested that aPDT can reduce biofilm thickness, disrupt biofilm attachment from ETT surface and kill microbial cells. These data suggest that aPDT should be investigated to decrease VAP incidence via ETT decontamination.     

Structures and Stability of Complexes of E(C6F5)3 (E = B,Al, Ga,In) with Acetonitrile

Complexes formed by interaction of E(C₆F₅)₃ (E = B, Al, Ga, In) with excess of acetonitrile (AN) were structurally characterized. Quantum chemical computations indicate that for Al(C₆F₅)₃ and In(C₆F₅)₃ the formation of a complex of 1:2 composition is more advantageous than for B(C₆F₅)₃ and Ga(C₆F₅)₃, in line with experimental observations. Formation of the solvate [Al(C₆F₅)₃ · 2AN] · AN is in agreement with predicted thermodynamic instability of [Al(C₆F₅)₃ · 3AN]. Tensimetry study of B(C₆F₅)₃ · CH₃CN reveals its stability in the solid state up to 197 °C. With the temperature increase, the complex undergoes irreversible thermal decomposition with pentafluorobenzene formation.     

Structural and energetic properties of RMX3-NH3 complexes

We have explored the structural and energetic properties of a series of RMX₃-NH₃ (M=Si, Ge; X=F, Cl; R=CH₃, C₆H₅) complexes using density functional theory and low-temperature infrared spectroscopy. In the minimum-energy structures, the NH₃ binds axially to the metal, opposite a halogen, while the organic group resides in an equatorial site. Remarkably, the primary mode of interaction in several of these systems seems to be hydrogen bonding (C-H--N) rather than a tetrel (N→M) interaction. This is particularly clear for the RMCl₃-NH₃ complexes, and analyses of the charge distributions of the acid fragment corroborate this assessment. We also identified a set of metastable geometries in which the ammonia binds opposite the organic substituent in an axial orientation. Acid fragment charge analyses also provide a clear rationale as to why these configurations are less stable than the minimum-energy structures. Matrix-isolation infrared spectra provide clear evidence for the occurrence of the minimum-energy form of CH₃SiCl₃–NH₃, but analogous results for CH₃GeCl₃–NH₃ are less conclusive. Computational scans of the M-N distance potentials for CH₃SiCl₃–NH₃ and CH₃GeCl₃–NH₃, both in the gas phase and bulk dielectric media, reveal a great deal of anharmonicity and a propensity for condensed-phase structural change.     

Quadruplex–Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands

A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5′- or 3′-terminus to mimic a quadruplex–duplex (Q–D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q–D hybrids with a very high affinity in the order K_a≈10⁷ m ⁻¹ irrespective of the duplex location at the quadruplex 3′- or 5′-end. NMR chemical shift perturbations identified the tetrad face of the Q–D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3′- or 5′-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3′-Q–D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5′-Q–D hybrid.     

How mobile NMR can help with the conservation of paintings

The conservation of paintings is fundamental to ensure that future generations will have access to the ideas of the grand masters who created these art pieces. Many factors, such as humidity, temperature, light, and pollutants, pose a risk to the conservation of paintings. To help with painting conservation, it is essential to be able to noninvasively study how these factors affect paintings and to develop methods to investigate their effects on painting degradation. Hence, the use of mobile nuclear magnetic resonance (NMR) as a method of investigation of paintings is gaining increased attention in the world of Heritage Science. In this mini-review, we discuss how this method was used to better understand the stratigraphy of paintings and the effect different factors have on the painting integrity, to analyze the different cleaning techniques suitable for painting conservation, and to show how mobile NMR can be used to identify forgeries. It is also important to keep in mind its limitations and build upon this information to optimize it to extend its applicability to the study of paintings and other precious objects of cultural heritage.