Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors

SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CL^pro or M^pro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CL^pro active site. These compounds will facilitate further 3CL^pro inhibitor design.     

Charge‐Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy

Adenosine radicals tagged with a fixed‐charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born–Oppenheimer molecular dynamics, ab initio, and excited‐state calculations led to unambiguous assignment of adenosine radicals as N‐7 hydrogen atom adducts. The charge‐tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.     

The 1:1 glycine zwitterion-water complex: An ab initio electronic structure study

More than a dozen stationary points on the potential energy surface for the 1:1 glycine zwitterion—water complex have been investigated at Hartree-Fock or MP2 levels of theory with basis sets ranging from split valence (4-31G) to split valence plus polarization and diffuse function (6–31 + + G**) quality. Only one true minimum (GLYZWM, C₁ symmetry) could be located on the potential energy surface. GLYZWM features a bridged water molecule acting as both a hydrogen bond acceptor and donor with the NH₃⁻ and CO₂⁻ units of the glycine zwitterion. The total hydrogen bond energy in GLYZWM is computed as 16 kcal/mol (MP2/6–31 ++ G** // 6–31 ++ G**, including corrections for basis set superpositions errors). The computed vibrational frequencies and normal mode forms of the GLYZWM complex resemble in many cases experimental assignments made for the glycine zwitterion in bulk water on the basis of Raman spectroscopy. © 1996 by John Wiley & Sons, Inc.     

Polymetacrylate and hybrid interparticle monolithic columns for fast separations of proteins by capillary liquid chromatography

Preparation of organic polymer monolithic columns in fused silica capillaries was aimed at fast gradient separation of proteins. For this purpose, polymerization in situ procedure was optimized, using ethylene dimetacrylate and butyl metacrylate monomers with azobisisobutyronitrile as initiator of the polymerization reaction in presence of non-aqueous porogen solvent mixtures composed of 1-propanol and 1,4-butanediol. The separation of proteins in totally monolithic capillary columns was compared with the chromatography on a new type of "hybrid interparticle monolithic" capillary columns, prepared by in situ polymerization in capillary packed with superficially porous spherical beds, 37-50 microm. The "hybrid" columns showed excellent stability and improved hydrodynamic flow properties with respect to the "totally" monolithic capillary columns. The separation selectivity is similar in the two types of columns. The nature of the superficially porous layer (bare silica or bonded C18 ligands) affects the separation selectivity less significantly than the porosity (density) of the monolithic moiety in the interparticle space, controlled by the composition of the polymerization mixture. The retention behaviour of proteins on all prepared columns is consistent with the reversed-phase gradient elution theory.     

Magnetically Enhanced 15 kHz Glow Discharge of Methane

This work deals with the luminous chemical vapour deposition (plasma polymerization) of hydrocarbon polymeric thin films in a magnetic field enhanced discharge of methane. The films were deposited on 4″ <111> single crystal silicon substrates. We investigated the influence of the different glow discharge parameters (e.g. pressure, flow rate, power input, etc.) on the deposition rate of methane and the refractive index of the resulting polymeric films, as well as the distribution of these parameters across the wafer. We used a Shinko Seiki Plasma Polymerization equipment with a bell jar reactor comprising two electrodes connected to a symmetric AC power supply of 15 kHz. Two magnetrons were formed by placing two circular shaped concentric magnetic poles behind each electrode. The substrates were attached on both sides of a rotating wheel held at a floating potential in the middle of the two electrodes. This equipment allowed us to vary a single parameter and keep the other parameters constant over the whole process. We measured the thickness and the refractive index and their distribution over the wafer. The effect of the system pressure, decoupled from the effect of flow rate, is explained by the characteristic nature of luminous gas phase and by the polymerization/deposition mechanism of luminous chemical vapour deposition.     

GpdA-promoter-controlled production of glucose oxidase by recombinant aspergillus niger using nonglucose carbon sources

The gpdA-promoter-controlled exocellular production of glucose oxidase (GOD) by recombinant Aspergillus niger NRRL-3 (GOD3-18) during growth on glucose and nonglucose carbon sources was investigated. Screening of various carbon substrates in shake-flask cultures revealed that exocellular GOD activities were not only obtained on glucose but also during growth on mannose, fructose, and xylose. The performance of A. niger NRRL-3 (GOD3-18) using glucose, fructose, or xylose as carbon substrate was compared in more detail in bioreactor cultures. These studies revealed that gpdA-promoter-controlled GOD synthesis was strictly coupled to cell growth. The gpdA-promoter was most active during growth on glucose. However, the unfavorable rapid GOD-catalyzed transformation of glucose into gluconic acid, a carbon source not supporting further cell growth and GOD production, resulted in low biomass yields and, therefore, reduced the advantageous properties of glucose. The total (endo- and exocellular) specific GOD activities were lowest when growth occurred on fructose (only a third of the activity that was obtained on glucose), whereas utilization of xylose resulted in total specific GOD activities nearly as high as reached during growth on glucose. Also, the portion of GOD excreted into the culture fluid reached similar high levels (≅ 90%) by using either glucose or xylose as substrate, whereas growth on fructose resulted in a more pelleted morphology with more than half the total GOD activity retained in the fungal biomass. Finally, growth on xylose resulted in the highest biomass yield and, consequently, the highest total volumetric GOD activity. These results show that xylose is the most favorable carbon substrate for gpdA-promoter-controlled production of exocellular GOD.     

Novel Methods to Manipulate Autolysis in Sparkling Wine: Effects on Yeast

Sparkling wine made by the traditional method (Méthode Traditionelle) develops a distinct and desirable flavour and aroma profile attributed to proteolytic processes during prolonged ageing on lees. Microwave, ultrasound and addition of β-glucanase enzymes were applied to accelerate the disruption of Saccharomyces cerevisiae, and added to the tirage solution for secondary fermentation in traditional sparkling winemaking. Scanning electron microscopy and flow cytometry analyses were used to observe and describe yeast whole-cell anatomy, and cell integrity and structure via propidium iodide (PI) permeability after 6-, 12- and 18-months post-tirage. Treatments applied produced features on lees that were distinct from that of the untreated control yeast. Whilst control yeast displayed budding cells (growth features) with smooth, cavitated and flat external cell appearances; microwave treated yeast cells exhibited modifications like ‘doughnut’ shapes immediately after treatment (time 0). Similar ‘doughnut’-shaped and ‘pitted/porous’ cell features were observed on progressively older lees from the control. Flow cytometry was used to discriminate yeast populations; features consistent with cell disruption were observed in the microwave, ultrasound and enzyme treatments, as evidenced by up to 4-fold increase in PI signal in the microwave treatment. Forward and side scatter signals reflected changes in size and structure of yeast cells, in all treatments applied. When flow cytometry was interpreted alongside the scanning electron microscopy images, bimodal populations of yeast cells with low and high PI intensities were revealed and distinctive ‘doughnut’-shaped cell features observed in association with the microwave treatment only at tirage, that were not observed until 12 months wine ageing in older lees from the control. This work offers both a rapid approach to visualise alterations to yeast cell surfaces and a better understanding of the mechanisms of yeast lysis. Microwave, ultrasound or β-glucanase enzymes are tools that could potentially initiate the release of yeast cell compounds into wine. Further investigation into the impact of such treatments on the flavour and aroma profiles of the wines through sensory evaluation is warranted.