Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.     

Room Temperature Ionic Liquids in Asymmetric Hetero-Ene Type Reactions: Improving Organocatalyst Performance at Lower Temperatures

Room temperature ionic liquids (RTILs) have been widely used as (co)solvents in several catalytic processes modifying, in most of the cases, the catalyst activity and/or the selectivity for the studied reactions. However, there are just a few examples of their use in hydrogen bonding organocatalysis. In this paper, we show the positive effect of a set of imidazole-based ionic liquids ([bmim]BF₄ and [hmim]PF₆) in the enantioselective addition of formaldehyde tert-butylhydrazone to prochiral α-keto esters catalyzed by a sugar-based chiral thiourea. Reactions performed in the presence of low percentages of RTILs led to an increase of the catalyst activity, thereby making possible to work at lower temperatures. Thus, the chiral tert-butyl azomethyl tertiary alcohols could be obtained with moderate to good conversions and higher enantioselectivities for most of the studied substrates when using up to 30 vol% of [hmim]PF₆ as a cosolvent in processes performed in toluene.     

Fluorescence of New o‐Carborane Compounds with Different Fluorophores: Can it be Tuned?

Two sets of o‐carborane derivatives incorporating fluorene and anthracene fragments as fluorophore groups have been successfully synthesized and characterized, and their photophysical properties studied. The first set, comprising fluorene‐containing carboranes 6 – 9 , was prepared by catalyzed hydrosilylation reactions of ethynylfluorene with appropriate carboranylsilanes. The compound 1‐[(9,9‐dioctyl‐fluorene‐2‐yl)ethynyl]carborane ( 11 ) was synthesized by the reaction of 9,9‐dioctyl‐2‐ethynylfluorene and decaborane (B₁₀H₁₄). Furthermore, reactions of the lithium salt of 11 with 1 equivalent of 4‐(chloromethyl)styrene or 9‐(chloromethyl)anthracene yielded compounds 12 and 13 . Members of the second set of derivatives, comprising anthracene‐containing carboranes, were synthesized by reactions of monolithium or dilithium salts of 1‐Me‐1,2‐C₂B₁₀H₁₁, 1‐Ph‐1,2‐C₂B₁₀H₁₁, and 1,2‐C₂B₁₀H₁₂ with 1 or 2 equivalents of 9‐(chloromethyl)anthracene, respectively, to produce compounds 14 – 16 . In addition, 2 equivalents of the monolithium salts of 1‐Me‐1,2‐C₂B₁₀H₁₁ (Me‐o‐carborane) and 1‐Ph‐1,2‐C₂B₁₀H₁₁ (Ph‐o‐carborane) were reacted with 9,10‐bis(chloromethyl)anthracene to produce compounds 17 and 18 , respectively. Fluorene derivatives 6 – 9 exhibit moderate fluorescence quantum yields (32–44 %), whereas 11 – 13 , in which the fluorophore is bonded to the C_cluster (C_c), show very low emission intensity (6 %) or complete fluorescence quenching. The anthracenyl derivatives containing the Me‐o‐carborane moiety exhibit notably high fluorescence emissions, with ?_F=82 and 94 %, whereas their Ph‐o‐carborane analogues are not fluorescent at all. For these compounds, we have observed a correlation between the C_c?C_c bond length and the fluorescence intensity in CH₂Cl₂ solution, comparable to that observed for previously reported styrene‐containing carboranes. Thus, our hypothesis is that for systems of this type the fluorescence may be tuned and even predicted by changing the substituent on the adjacent C_c.     

Magnetobiosensors Based on Viral Protein p19 for MicroRNA Determination in Cancer Cells and Tissues

MicroRNAs (miRs) have emerged as important clinical biomarkers with both diagnostic and prognostic value for relevant diseases, such as cancer. MiRs pose unique challenges for detection and are currently detected by northern blotting, real‐time PCR, and microarray techniques. These expensive, complicated, and time‐consuming techniques are not feasible for on‐site miR determination. In this study, amperometric magnetobiosensors involving RNA‐binding viral protein p19 as a selective biorecognition element were developed for miR quantification. The p19‐based magnetosensors were able to detect 0.4 fmol of a synthetic target and endogenous miR‐21 (selected as a model for its role in a wide variety of cancers) in only 2 h in total RNA extracted from cancer cells and human breast‐tumor specimens without PCR amplification and sample preprocessing. These results open up formidable perspectives for the diagnosis and prognosis of human cancers and for drug‐discovery programs.     

Memory Effects in High-Dimensional Systems Faithfully Identified by Hilbert–Schmidt Speed-Based Witness

A witness of non-Markovianity based on the Hilbert–Schmidt speed (HSS), a special type of quantum statistical speed, has been recently introduced for low-dimensional quantum systems. Such a non-Markovianity witness is particularly useful, being easily computable since no diagonalization of the system density matrix is required. We investigate the sensitivity of this HSS-based witness to detect non-Markovianity in various high-dimensional and multipartite open quantum systems with finite Hilbert spaces. We find that the time behaviors of the HSS-based witness are always in agreement with those of quantum negativity or quantum correlation measure. These results show that the HSS-based witness is a faithful identifier of the memory effects appearing in the quantum evolution of a high-dimensional system with a finite Hilbert space.     

Secondary Metabolites,including a New 5,6-Dihydropyran-2-One,Produced by the Fungus Diplodia corticola. Aphicidal Activity of the Main Metabolite,Sphaeropsidin A

An undescribed 5,6-dihydropyran-2-one, namely diplopyrone C, was isolated and characterized from the cultures of an isolate of the fungus Diplodia corticola recovered from Quercus suber in Algeria. The structure and relative stereostructure of (5S,6S,7Z,9S,10S)-5-hydroxy-6-(2-(3-methyloxiran-2-yl)vinyl)-5,6-dihydro-2H-pyran-2-one were assigned essentially based on NMR and MS data. Furthermore, ten known compounds were isolated and identified in the same cultures. The most abundant product, the tetracyclic pimarane diterpene sphaeropsidin A, was tested for insecticidal effects against the model sucking aphid, Acyrthosiphon pisum. Results showed a toxic dose-dependent oral activity of sphaeropsidin A, with an LC₅₀ of 9.64 mM.     

Production and Digestibility Studies of β-Galactosyl Xylitol Derivatives Using Heterogeneous Catalysts of LacA β-Galactosidase from Lactobacillus Plantarum WCFS1

The synthesis of β-galactosyl xylitol derivatives using immobilized LacA β-galactosidase from Lactobacillus plantarum WCFS1 is presented. These compounds have the potential to replace traditional sugars by their properties as sweetener and taking the advantages of a low digestibility. The enzyme was immobilized on different supports, obtaining immobilized preparations with different activity and stability. The immobilization on agarose-IDA-Zn-CHO in the presence of galactose allowed for the conserving of 78% of the offered activity. This preparation was 3.8 times more stable than soluble. Since the enzyme has polyhistidine tags, this support allowed the immobilization, purification and stabilization in one step. The immobilized preparation was used in synthesis obtaining two main products and a total of around 68 g/L of β-galactosyl xylitol derivatives and improving the synthesis/hydrolysis ratio by around 30% compared to that of the soluble enzyme. The catalyst was recycled 10 times, preserving an activity higher than 50%. The in vitro intestinal digestibility of the main β-galactosyl xylitol derivatives was lower than that of lactose, being around 6 and 15% for the galacto-xylitol derivatives compared to 55% of lactose after 120 min of digestion. The optimal amount immobilized constitutes a very useful tool to synthetize β-galactosyl xylitol derivatives since it can be used as a catalyst with high yield and being recycled for at least 10 more cycles.     

Development of Magnesium Anode-Based Transient Primary Batteries

Biodegradable primary batteries, also known as transient batteries, are essential to realize autonomous biodegradable electronic devices with high performance and advanced functionality. In this work, magnesium, copper, iron, and zinc – metals that exist as trace elements in the human body – were tested as materials for biomedical transient electronic devices. Different full cell combinations of Mg and X (where X = Cu, Fe, and Zn and the anodized form of the metals) with phosphate buffered saline (PBS) as electrolyte were studied. To form the cathodes, metal foils were anodized galvanostatically at a current density of 2.0 mA cm⁻² for 30 mins. Electrochemical measurements were then conducted for each electrode combination to evaluate full cell battery performance. Results showed that the Mg−Cu_anodized chemistry has the highest power density at 0.99 mW/cm². Nominal operating voltages of 1.26 V for the first 0.50 h and 0.63 V for the next 3.7 h were observed for Mg−Cu_anodized which was discharged at a current density of 0.70 mA cm⁻². Among the materials tested, Mg−Cu_anodized exhibited the best discharge performance with an average specific capacity of 2.94 mAh cm⁻², which is comparable to previous reports on transient batteries.     

Dynamic properties of soy globulin adsorbed films at the air-water interface

In this paper we present surface dilatational properties of soy globulins (beta-conglycinin, glycinin, and reduced glycinin with 10 mM of dithiothreitol (DTT)) adsorbed onto the air-water interface, as a function of adsorption time. The experiments were performed at constant temperature (20 degrees C), pH (8.0), and ionic strength (0.05 M). The surface rheological parameters were measured as a function of protein concentration (ranging from 1 to 1x10(-3)% wt/wt). We found that the surface dilatational modulus, E, increases, and the phase angle, phi, decreases with time, theta, which may be associated with protein adsorption. These phenomena have been related to protein adsorption, unfolding, and/or protein-protein interactions (at long-term adsorption) as a function of protein concentration in solution. From a rheological point of view, the surface viscoelastic characteristics of soy globulin films adsorbed at the air-water interface are practically elastic. The main conclusion is that the dilatational properties of the adsorbed films depend on the molecular structure of the protein.