Molecular docking and machine learning affinity prediction of compounds identified upon softwood bark extraction to the main protease of the SARS-CoV-2 virus

Molecular docking of 234 unique compounds identified in the softwood bark (W set) is presented with a focus on their inhibition potential to the main protease of the SARS-CoV-2 virus 3CL^pro (6WQF). The docking results are compared with the docking results of 866 COVID19-related compounds (S set). Furthermore, machine learning (ML) prediction of docking scores of the W set is presented using the S set trained TensorFlow, XGBoost, and SchNetPack ML approaches. Docking scores are evaluated with the Autodock 4.2.6 software. Four compounds in the W set achieve a docking score below −13 kcal/mol, with (+)-lariciresinol 9′-p-coumarate (CID 11497085) achieving the best docking score (−15 kcal/mol) within the W and S sets. In addition, 50% of W set docking scores are found below −8 kcal/mol and 25% below −10 kcal/mol. Therefore, the compounds identified in the softwood bark, show potential for antiviral activity upon extraction or further derivatization. The W set molecular docking studies are validated by means of molecular dynamics (five best compounds). The solubility (Log S, ESOL) and druglikeness of the best docking compounds in S and W sets are compared to evaluate the pharmacological potential of compounds identified in softwood bark.

Stability of Alum-Containing Paper under Alkaline Conditions

The present contribution evaluates the methods of degradation and stabilization of alum-containing paper with a focus on the alkaline environment achieved by deacidification procedures. In terms of reviewed subjects, the contribution focuses on alum-rosin sized paper, which is still used as a carrier of knowledge and information; however, it also mentions cellulose itself and other brands of paper. The contribution summarizes the results on the homogeneity of the distribution of alum and rosin in the paper mass and on the paper surface. It provides the knowledge gained in the field of alkaline hydrolysis and oxidation with special regard to transition metal species. It shows the values of alkaline reserves achieved in the main mass-deacidification processes. On the basis of the acquired knowledge, the contribution emphasizes the procedures of paper stabilization. Criteria of “increased mechanical permanence and lifetime prolongation” adopted to evaluate and compare the efficacy of individual mass-deacidification processes were applied and corresponding data are introduced. The contribution also draws attention to the existence of open issues in the area of paper degradation and stabilization.

Spruce Bark-A Source of Polyphenolic Compounds: Optimizing the Operating Conditions of Supercritical Carbon Dioxide Extraction

The present study described the optimization of the extraction process with carbon dioxide in supercritical state for obtaining extractives, especially polyphenols from softwood bark, Norway spruce (Picea abies (L.) Karst.). Using a full 2³ factorial design of experiments, the effect of varying the working parameters on the yield of extractives was studied for the following ranges: temperature 40-100 °C, pressure 1050-9000 psi (7.2-62 MPa), and concentration of EtOH/water co-solvent mixture 40-96.6%. In addition, total phenolics content and the antioxidant capacity of the spruce bark extract were determined. The optimum operating conditions for the yield of extractives were identified as 73 °C, 6465 psi (44.5 MPa), and 58% EtOH/water cosolvent concentration for a yield of 8.92%. The optimum conditions for achieving a total phenolics content of 13.89 mg gallic acid equivalent (GAE)/g dry extract were determined as: 45 °C, 1050 psi (7.2 MPa), and 96.6% EtOH/water mixture.

Use of Deep Eutectic Solvents in Polymer Chemistry-A Review

This review deals with two overlapping issues, namely polymer chemistry and deep eutectic solvents (DESs). With regard to polymers, specific aspects of synthetic polymers, polymerization processes producing such polymers, and natural cellulose-based nanopolymers are evaluated. As for DESs, their compliance with green chemistry requirements, their basic properties and involvement in polymer chemistry are discussed. In addition to reviewing the state-of-the-art for selected kinds of polymers, the paper reveals further possibilities in the employment of DESs in polymer chemistry. As an example, the significance of DES polarity and polymer polarity to control polymerization processes, modify polymer properties, and synthesize polymers with a specific structure and behavior, is emphasized.

Antibacterial and antifungal activity of phytosterols and methyl dehydroabietate of Norway spruce bark extracts

The current study focuses on the analysis of in vitro biological activity of extract from bark of Norway spruce (Picea Abies), which can find potential application in food and cosmetic industry and pharmacology. Milled bark was subjected to Soxhlet extraction and supercritical fluid extraction to obtain two ethanol extracts. These extracts were further used to obtain their pre-extracts to n-hexane. It was investigated whether beta-sitosterol exhibits bacteriostatic activity necessary to observe antimicrobial and antifungal activity of methyl dehydroabiatate. This synergic effect and bacteriostatic activity of beta-sitosterol have not been previously reported. The greatest inhibition zone of n-hexane pre-extracts was confirmed in bacterium Pseudomonas aeruginosa (0,9 - 1,5 cm) and yeast Alternaria alternata (0,7 - 1,6 cm). It is novel, the antioxidant, antimicrobial and antifungal activity of spruce bark extracts assessed in terms of food and cosmetic fortification.

Composition of fatty acids and tocopherols in peels, seeds and leaves of Sea buckthorn

Peels, seeds and leaves of the Sea buckthorn were extracted by methanol and chloroform and characterized in terms of the fatty acids (FA) and tocopherol composition. All morphological parts of Sea buckthorn contained these biologically active compounds useful in medicine, pharmacology, human nutrition and cosmetics. The highest amount of α-tocopherol was found in peels (1103 mg kg-1). The lowest content of α-tocopherol was found in leaves (659 mg kg-1). Delta-tocopherol was found in higher amount in peels 1757 mg kg-1. Seeds contained 95 mg kg-1 of delta-tocopherols. Gamma-tocopherol was found in seeds (459 mg kg-1), peels (188 mg kg-1) and in leaves (587 mg kg-1). β-tocopherol was present only in seeds (171 mg kg-1). Unsaturated fatty acids were dominant in all morphological parts of Sea buckthorn. The highest amounts of unsaturated fatty acids (92 rel. %) were determined in seeds. Dominant fatty acids of seeds were linoleic acid (37 %), α-linolenic acid (30 %) and vaccenic acid (20 %). Leaves were rich in α-linolenic acid (51 %). Dominant fatty acids of peels were oleic acid (16 %), palmitic acid (33 %) and palmitoleic acid (29 %).

Energy and chemical conversion of five Australian lignocellulosic feedstocks into bio-crude through liquefaction

Thermal liquefaction of five potential feedstocks namely, banana bunch stems (BBS), pineapple tops (PT), Forage sorghum (FS), bagasse (Ba) and Arundo donax (AD) were examined from an energy perspective at a large laboratory scale.

Characterization of Klason lignins by reversed-phase high-performance liquid chromatography using wide-pore octadecylsilica and stepwise gradients of dimethylformamide in water

RP-HPLC using stepwise gradients of N,N-dimethylformamide (DMF) in a phosphate-buffered (pH 3.00) aqueous mobile phase and a wide-pore (30 nm) octadecylsilica column has been applied to the analysis of a variety of lignins--organocell lignin, dioxane lignin, Björkman lignin, and Klason lignins from both softwoods and hardwoods, respectively, in order to demonstrate the usefulness of the approach for their characterization. Tandem combination of spectrophotometric diode array detection and fluorimetric detection was used to acquire more detailed information about the chromatographic behavior of lignins. The results show that a ten-step gradient can reveal distinct features of lignins and humic substances. Combination of good solvating properties of DMF for lignins together with a wide-pore RP sorbent improves surface interactions of the analytes and suppresses the influence of size exclusion effects. Thus it provides reproducibility of characterization profiles and robustness of the method. The calculated repeatability of the retention time of selected peaks was +/- 0.46% RSD. The reproducibility of the data within one week (set of seven data) was +/- 1.1% RSD. These data are also representative of the other well-shaped peaks of analyzed substances.