Production of hydrophobic amino acids from biobased resources: wheat gluten and rubber seed proteins

Identifying Novel Therapeutics for the Resistant Mutant "F533L" in PBP3 of Pseudomonas aeruginosa Using ML Techniques

Pseudomonas aeruginosa (P. aeruginosa) is a highly infectious and antibiotic-resistant bacterium, which causes acute and chronic nosocomial infections. P. aeruginosa exhibits multidrug resistance due to the emergence of resistant mutants. The bacterium takes advantage of intrinsic and acquired resistance mechanisms to resist almost every antibiotic. To overcome the drug-resistance problem, there is a need to develop effective drugs against antibiotic-resistant mutants. Therefore, in this study, we selected the F533L mutation in PBP3 (penicillin-binding protein 3) because of its important role in β-lactam recognition. To target this mutation, we screened 147 antibacterial compounds from PubChem through a machine-learning model developed based on the decision stump algorithm with 75.75% accuracy and filtered out 55 compounds. Subsequently, out of 55 compounds, 47 compounds were filtered based on their drug-like activity. These 47 compounds were subjected to virtual screening to obtain binding affinity compounds. The binding affinity range of all 47 compounds was -11.3 to -4.6 kcal mol-1. The top 10 compounds were examined according to their binding with the mutation point. A molecular dynamic simulation of the top 8 compounds was conducted to understand the stability of the compounds containing the mutated PBP3. Out of 8 compounds, 3 compounds, namely, macozinone, antibacterial agent 71, and antibacterial agent 123, showed good stability and were validated by RMSD, RMSF, and binding-free analysis. The findings of this study revealed promising antibacterial compounds against the F533L mutant PBP3. Furthermore, developments in these compounds may pave the way for novel therapeutic interventions.

Characterization of Yeast Protein Hydrolysate for Potential Application as a Feed Additive

Yeast protein can be a nutritionally suitable auxiliary protein source in livestock food. The breakdown of proteins and thereby generating high-quality peptide, typically provides nutritional benefits. Enzyme hydrolysis has been effectively uesed to generate peptides; however, studies on the potential applications of different types of enzymes to produce yeast protein hydrolysates remain limited. This study investigated the effects of endo- (alcalase and neutrase) and exotype (flavourzyme and prozyme 2000P) enzyme treatments on yeast protein. Endotype enzymes facilitate a higher hydrolysis efficiency in yeast proteins than exotype enzymes. The highest degree of hydrolysis was observed for the protein treated with neutrase, which was followed by alcalase, prozyme 2000P, and flavourzyme. Furthermore, endotype enzyme treated proteins exhibited higher solubility than their exotype counterparts. Notably, the more uniform particle size distribution was observed in endotype treated yeast protein. Moreover, compared with the original yeast protein, the enzymatic protein hydrolysates possessed a higher content of β-sheets structures, indicating their higher structural stability. Regardless of enzyme type, enzyme treated protein possessed a higher total free amino acid content including essential amino acids. Therefore, this study provides significant insights into the production of protein hydrolysates as an alternative protein material.

High-sensitivity profiling of dipeptides in sauce-flavor Baijiu Daqu by chemical derivatization and ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry

Dipeptides in sauce-flavor Baijiu Daqu are protein degradation products during the fermentation of Daqu, which are believed to play a crucial role in the flavor and quality of Baijiu. Herein, we integrated dansyl chloride derivatization with ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) for comprehensively profiling dipeptides in Daqu. The derivatization efficiency was higher than 99.1 % for all 17 dipeptide standards under the optimized derivatization conditions. In total, 118 dipeptides were detected in Daqu. The method was validated and the analytical characteristics including the linearity (spanned across 2-4 orders of magnitude), precision (1.2-19.9 %), limit of detection (varied from 1.1 to 53.4 pmol/mL) and the stability (3.6-15.8 %) are satisfactory. The usefulness of the method was examined by studying the distribution characteristics of dipeptides in Daqu under different production conditions. The present method provides an effective and robust strategy for comprehensively analyzing dipeptide compounds in complex biological samples.

A computational study of structural analysis of Class I human glucose-6-phosphate dehydrogenase (G6PD) variants: Elaborating the correlation to chronic non-spherocytic hemolytic anemia (CNSHA)

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect that affects more than 500 million people worldwide. Individuals affected with G6PD deficiency may occasionally suffer mild-to-severe chronic hemolytic anemia. Chronic non-spherocytic hemolytic anemia (CNSHA) is a potential result of the Class I G6PD variants. This comparative computational study attempted to correct the defect in variants structure by docking the AG1 molecule to selected Class I G6PD variants [G6PD^Nashville (Arg393His), G6PD^Alhambra (Val394Leu), and G6PD^Durham (Lys238Arg)] at the dimer interface and structural NADP⁺ binding site. It was followed by an analysis of the enzyme conformations before and after binding to the AG1 molecule using the molecular dynamics simulation (MDS) approach, while the severity of CNSHA was determined via root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), hydrogen bonds, salt bridges, radius of gyration (Rg), solvent accessible surface area analysis (SASA), and principal component analysis (PCA). The results revealed that G6PD^Nashville (Arg393His) and G6PD^Durham (Lys238Arg) had lost the direct contact with structural NADP⁺ and salt bridges at Glu419 - Arg427 and Glu206 - Lys407 were disrupted in all selected variants. Furthermore, the AG1 molecule re-stabilized the enzyme structure by restoring the missing interactions. Bioinformatics approaches were also used to conduct a detailed structural analysis of the G6PD enzyme at a molecular level to understand the implications of these variants toward enzyme function. Our findings suggest that despite the lack of treatment for G6PDD to date, AG1 remains a novel molecule that promotes activation in a variety of G6PD variants.

Characteristics of Biofoam Cups Made from Sugarcane Bagasse with Rhizopus oligosporus as Binding Agent

This study is aimed at producing a biofoam cup made from sugarcane bagasse with tempeh mold (Rhizopus oligosporus). Soybean flour (SF) was added to promote the growth of mycelia, which could bind the bagasse fiber matrix. The main materials were whole bagasse (B) and depithed bagasse (DB). The SF weight ratios to bagasse were 1 : 1 (SF1) and 1.5 : 1 (SF1.5). Therefore, the studied specimens were labeled B-SF1, DB-SF1, B-SF1.5, and DB-SF1.5. All biofoam cups were analyzed for their physical properties (water absorption and porosity), mechanical properties (puncture and compressive strengths), biodegradability, and thermal properties (thermogravimetric analysis). The lowest water absorption rates were obtained from the B biofoam cups ( $23\%\pm 2.45\%$ ) and the SF1.5 biofoam cups ( $25.83\%\pm 5.19\%$ ). Both B-SF1 and B-SF1.5 had lower porosity ( $8.72\%\pm 0.88\%$ and $10.77\%\pm 1.54\%$ , respectively) than the DB biofoam cups. Moreover, the B biofoam cups had smoother biofoam surfaces, smaller voids, and lower porosity compared with the DB samples. However, the DB biofoam cups showed the highest puncture strength ( $2.95\pm 0.37$  kg cm−2) among all samples. Nevertheless, the B-SF1.5 biofoam cup had the highest compressive strength ( $3.98\pm 0.39$  MPa) and the DB-SF1.5 exhibited the slowest degradation rate ( $27\%\pm 0.7\%$ ) after 14 days of soil burial. The highest thermal stability was obtained from B-SF1.5, which had a thermal degradation temperature of 264°C. Overall, B-SF1.5 had the smoothest surface, good thermal stability, and high compressive strength.

Taurine, homotaurine, GABA and hydrophobic amino acids content influences "in vitro" antioxidant and SIRT1 modulation activities of enzymatic protein hydrolysates from algae

Prevention and control of diseases and delaying the signs of ageing are nowadays one of the major goals of biomedicine. Sirtuins, a family of NAD⁺ dependent deacylase enzymes, could be pivotal targets of novel preventive and therapeutic strategies to achieve such aims. SIRT1 activating and inhibiting compounds, such as polyphenols and bioactive peptides, have been proposed to be involved in the development of many human diseases. The objective of this work was to assess and compare the antioxidant and SIRT1 modulation activities of enzymatic protein hydrolysates (EPHs) from a wide number of algae species (24 commercial samples and 12 samples harvested off the Atlantic coast of northern Spain). High antioxidant activities were observed in EPHs from red and green seaweed species. Moreover, 19 samples exhibited SIRT1 activation, while EPHs from the 16 samples were SIRT1 inhibitors. Pearson's correlation test and Principal Component Analysis revealed significant correlations between (1) total peptide and hydrophobic amino acid content in EPHs and their antioxidant activities, and (2) concentrations of taurine, homotaurine, and amino acid gamma aminobutyric acid in EPHs and their SIRT1 modulation activity.

Fluorinated Protein and Peptide Materials for Biomedical Applications

Fluorination represents one of the most powerful modern design strategies to impart biomacromolecules with unique functionality, empowering them for widespread application in the biomedical realm. However, the properties of fluorinated protein materials remain unpredictable due to the heavy context-dependency of the surrounding atoms influenced by fluorine’s strong electron-withdrawing tendencies. This review aims to discern patterns and elucidate design principles governing the biochemical synthesis and rational installation of fluorine into protein and peptide sequences for diverse biomedical applications. Several case studies are presented to deconvolute the overgeneralized fluorous stabilization effect and critically examine the duplicitous nature of the resultant enhanced chemical and thermostability as it applies to use as biomimetic therapeutics, drug delivery vehicles, and bioimaging modalities.

Subcritical water as hydrolytic medium to recover and fractionate the protein fraction and phenolic compounds from craft brewer's spent grain

The valorization of the brewer's spent grain (BSG) generated in a craft beer industry was studied by subcritical water hydrolysis in a semi-continuous fixed-bed reactor. Temperature was varied from 125 to 185 °C at a constant flow rate of 4 mL/min. Biomass hydrolysis yielded a maximum of 78% of solubilized protein at 185 °C. Free amino acids presented a maximum level at 160 °C with a value of 55 mg free amino acids/g_protein-BSG. Polar amino acid presented a maximum at lower temperatures than non-polar amino acids. The maximum in total phenolic compounds was reached at 185 °C. This maximum is the same for aldehyde phenolic compounds such as vanillin, syringic and protocatechuic aldehyde; however, for hydroxycinnamic acids, such as ferulic acid and p-coumaric, the maximum was obtained at 160 °C. This allows a fractionation of the bioactive compounds. Subcritical water addresses opportunities for small breweries to be incorporated within the biorefinery concept.

Facile continuous production of soy peptide nanogels via nanoscale flash desolvation for drug entrapment

A facile continuous production of soy peptide nanogels was demonstrated using a multi-inlet vortex micromixer for the entrapment of active ingredients. The full flow regime in the micromixer was systematically studied to understand the flow impact on nanogel size, drug encapsulation efficiency and drug loading efficiency. Ibuprofen was chosen as a model drug to demonstrate encapsulation capability. The study showed that the nanogel size, drug encapsulation efficiency and drug loading efficiency did not alter significantly as long as the flow rates were in transition and turbulent regimes. The driving force behind the folding of peptides within the microenvironment is kinetic mixing with high flow rates, which dominates in comparison to molecular diffusion, nucleation, and growth. Moreover, the hydrophilic-lipophilic balance of the soy peptides determined the drug encapsulation efficiency and the drug loading efficiency, which did not vary much under different manufacturing parameters. Both characteristics are beneficial to mass production of drug-entrapped peptide. In a 50% water-ethanol mixture, the encapsulation efficiency achieved 70% and the drug loading efficiency was up to 25% in transition and turbulent flow regimes. This work opens the avenues to continuous production of drug-entrapped soy peptide nanogels using a multi-inlet vortex micromixer.