In Silico, Molecular Docking and In Vitro Antimicrobial Activity of the Major Rapeseed Seed Storage Proteins

Purification and Identification of Novel Dipeptidyl Peptidase IV Inhibitory Peptides Derived from Bighead Carp (Hypophthalmichthys nobilis)

Dipeptidyl peptidase IV (DPP-IV) inhibitors are widely used in treating type 2 diabetes due to their ability to lower blood glucose levels. However, synthetic versions often lead to gastrointestinal side effects. This study explores DPP-IV inhibitory properties in peptides from bighead carp skin. Collagen was prepared, hydrolyzed into collagen peptides, and then fractionated for DPP-IV inhibitory activity examination. The most effective fractions were identified, and their peptide sequences were determined. Molecular docking analysis identified nine peptides with potential inhibitory activity, four of which (VYP, FVA, PPGF, PGLVG) were synthesized and tested in vitro. PPGF exhibited the highest potency with an IC50 of 4.63 nM, competitively binding to key DPP-IV sites, including ARG125, VAL711, TYR666, and TYR662. Other peptides showed varying effectiveness, with IC50 values of 398.87 nM (VYP), 402.02 nM (FVA), and 110.20 nM (PGLVG). These findings highlight bighead carp skin peptides as potent DPP-IV inhibitors with hypoglycemic potential, suggesting a novel avenue for diabetes management using natural peptides. Moreover, this research underscores the utilization of bighead carp by-products, contributing to environmental sustainability.

Brassicaceae Mustards: Phytochemical Constituents, Pharmacological Effects, and Mechanisms of Action against Human Disease

The Brassicaceae genus consists of many economically important mustards of value for food and medicinal purposes, namely Asian mustard (Brassica juncea), ball mustard (Neslia paniculata), black mustard (B. nigra), garlic mustard (Alliaria petiolata), hedge mustard (Sisymbrium officinale), Asian hedge mustard (S. orientale), oilseed rape (B. napus), rapeseed (B. rapa), treacle mustard (Erysimum repandum), smooth mustard (S. erysimoides), white ball mustard (Calepina irregularis), white mustard (Sinapis alba), and Canola. Some of these are commercially cultivated as oilseeds to meet the global demand for a healthy plant-derived oil, high in polyunsaturated fats, i.e., B. napus and B. juncea. Other species are foraged from the wild where they grow on roadsides and as a weed of arable land, i.e., E. repandum and S. erysimoides, and harvested for medicinal uses. These plants contain a diverse range of bioactive natural products including sulfur-containing glucosinolates and other potentially valuable compounds, namely omega-3-fatty acids, terpenoids, phenylpropanoids, flavonoids, tannins, S-methyl cysteine sulfoxide, and trace-elements. Various parts of these plants and many of the molecules that are produced throughout the plant have been used in traditional medicines and more recently in the mainstream pharmaceutical and food industries. This study relates the uses of mustards in traditional medicines with their bioactive molecules and possible mechanisms of action and provides an overview of the current knowledge of Brassicaceae oilseeds and mustards, their phytochemicals, and their biological activities.

Identifying and characterization of novel broad-spectrum bacteriocins from the Shanxi aged vinegar microbiome: Machine learning, molecular simulation, and activity validation

Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this study was to mine, screen and characterize novel broad-spectrum bacteriocins from the large-scale microbiome data of Shanxi aged vinegar through machine learning, molecular simulation and activity validation. A total of 158 potential bacteriocins were innovatively mined from 117,552 representative genes based on metatranscriptomic information from the Shanxi aged vinegar microbiome using machine learning techniques and 12 microorganisms were identified to secrete bacteriocins at the genus level. Subsequently, employing AlphaFold2 structure prediction and molecular dynamics simulations, eight bacteriocins with high stability were further screened, and all of them were confirmed to have bacteriostatic activity by the Escherichia coli BL21 expression system. Then, gene_386319 (named LAB-3) and gene_403047 (named LAB-4) with the strongest antibacterial activities were purified by two-step methods and analyzed by mass spectrometry. The two bacteriocins have broad-spectrum antimicrobial activity with minimum inhibitory concentration values of 6.79 μg/mL-15.31 μg/mL against Staphylococcus aureus and Escherichia coli. Furthermore, molecular docking analysis indicated that LAB-3 and LAB-4 could interact with dihydrofolate reductase through hydrogen bonds, salt-bridge forces and hydrophobic forces. These findings suggested that the two bacteriocins could be considered as promising broad-spectrum antimicrobial agents.

The Phenolic Content of Pistacia lentiscus Leaf Extract and Its Antioxidant and Antidiabetic Properties

The aims of this study were to determine the polyphenolic profile, to estimate the total phenolic and flavonoid contents, and to evaluate the antioxidant and antidiabetic activities of the extract of Pistacia lentiscus leaves, and the hydroacetonic mixture was employed as an alternative for common solvents in the extraction process. In order to explain the antidiabetic activity, molecular docking has been performed on the main constituents of the leaf extract. The characterization of the extract has been performed by high-performance liquid chromatography (HPLC) leading to the detection of 20 compounds of which gallic acid, ellagic acid, catechin, kaempferol, and quercetin 3-glucoside were identified using authentic standards. The total phenolic and flavonoid contents, assessed using the Folin-Ciocalteu and quercetin methods, were 394.5 ± 0.08 mg gallic acid equivalent/g dry extract (mg GAE/g DE) and 101.2 ± 0.095 mg quercetin equivalent/g dry extract (mg QE/g DE), respectively. On the other hand, the antioxidant activity of leaf extract, quantified by determining the ability to neutralize the free radical DPPH and β-carotene/linoleate model system, reached the values of 0.0027 ± 0.002 mg/mL and 0.128 ± 0.04 mg/mL, respectively. Regarding the antidiabetic activity, based on the inhibition of pancreatic α-amylase activity, a significant inhibition of about 68.20% with an IC50 value of 0.266 mg/mL had been observed. This finding is consistent with the molecular docking study of the main phenolic compounds of the extracts, where a remarkable binding affinity against α-amylase was observed, with values of -7.631 (kcal/mol), -6.818 (kcal/mol), and -5.517 (kcal/mol) for the major compounds catechin, quercetin-3-glucoside, and gallic acid, respectively.

Proteins from Blackberry Seeds: Extraction, Osborne Isolate, Characteristics, Functional Properties, and Bioactivities

Blackberry fruit contains high levels of nutrients and phenolic compounds. Blackberry pomace accounts for 20~30% of its whole fruit during processing and is generally treated as fertilizer. Blackberry pomace has many seeds that contain carbohydrates, polyphenols, flavonoids, pectin, protein, and other bioactive nutrients. However, its functional properties and seed protein compositions have not been reported. We used a single-factor experiment, response surface, and Osborne isolate method to extract protein isolate, albumin, globulin, glutelin, and prolamin from blackberry seeds for the first time and evaluated their characteristics and functional properties. Glutelin and protein isolate showed good water-holding capacity, emulsification, and foaming capacity, while albumin and globulin showed good oil-holding capacity and thermal stability. They were found to have good antioxidant activities that might be good DPPH free radical scavengers, especially prolamin, which has the lowest IC50 value (15.76 μg/mL). Moreover, globulin had the lowest IC50 value of 5.03 μg/mL against Hela cells, 31.82 μg/mL against HepG2 cells, and 77.81 μg/mL against MCF-7 cells and a high selectivity index (SI), which suggested globulin had better anti-cervical, antihepatoma, and anti-breast activity but relatively low cytotoxicity. These seed proteins may have great prospects for the development and application of food and drugs in the future.

Antioxidant, Cytotoxicity, Antimicrobial Activity, and In Silico Analysis of the Methanolic Leaf and Flower Extracts of Clitoria ternatea

Infectious diseases pose a significant threat to human health worldwide. To address this challenge, we conducted a comprehensive study on the leaf and flower extracts of Clitoria ternatea plants. Our research encompassed in vitro assessments of their antibacterial, antibiofilm, antioxidant, and cytotoxic properties. Additionally, we employed in silico screening to identify promising compounds with potential applications in developing novel anti-Escherichia coli medications. Notably, our investigation revealed a remarkable inhibition zone of 13.00 ± 1 mm when applying the leaf extract (200 μg/ml) against E. coli, showcasing its potent antibacterial properties. Furthermore, both the leaf and flower extracts exhibited substantial biofilm inhibition efficacy against S. aureus, with inhibition percentages of 54% and 58%, respectively. In the realm of antioxidant activity, the leaf and flower extracts of C. ternatea displayed noteworthy DPPH free radical scavenging capabilities. Specifically, the leaf extract exhibited a substantial activity of 62.39% at a concentration of 150 μg/ml, while the flower extract achieved 44.08% at the same concentration. Our study also evaluated the impact on brine shrimp, where the floral extract displayed a significantly higher mortality rate of 93.33% at a dosage of 200 μg/ml compared to the leaf extract. To elucidate potential therapeutic targets, we utilized molecular docking techniques, focusing on the acbR protein (5ENR) associated with antibiotic resistance in E. coli. In this analysis, compounds isolated from the C. ternatea leaf extract, namely D1 (CID-14478556), D2 (CID-6423376), and D3 (CID-20393), exhibited binding energies of -8.2 kcal/mol, -6.5 kcal/mol, and -6.3 kcal/mol, respectively. Additionally, compounds from the flower extract, E1 (CID-5282761), E2 (CID-538757), and E3 (CID-536762), displayed binding energies of -5.4 kcal/mol, -5.3 kcal/mol, and -5.1 kcal/mol, respectively. In conclusion, the leaf and flower extracts derived from C. ternatea represent a promising natural resource with potential therapeutic applications in combating antibiotic-resistant pathogens.

Neuroprotective efficacy of the bacterial metabolite, prodigiosin, against aluminium chloride-induced neurochemical alternations associated with Alzheimer's disease murine model: Involvement of Nrf2/HO-1/NF-κB signaling

Prodigiosin (PDG) is a bacterial metabolite with numerous biological and pharmaceutical properties. Exposure to aluminium is considered a root etiological factor in the pathological progress of Alzheimer's disease (AD). Here, in this investigation, we explored the neuroprotective potential of PDG against aluminium chloride (AlCl₃ )-mediated AD-like neurological alterations in rats. For this purpose, rats were gavaged either AlCl₃ (100 mg/kg), PDG (300 mg/kg), or both for 42 days. As a result of the analyzes performed on the hippocampal tissue, it was observed that AlCl₃ induced biochemical, molecular, and histopathological changes like those related to AD. PDG pre-treatment significantly decreased acetylcholinesterase activity and restored the levels of brain-derived neurotrophic factor, monoamines (dopamine, norepinephrine, and serotonin), and transmembrane protein (Na⁺ /K⁺ -ATPase). Furthermore, PDG boosted the hippocampal antioxidant capacity, as shown by the increased superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, and glutathione contents. These findings were accompanied by decreases in malondialdehyde and nitric oxide levels. The antioxidant effect may promote the upregulation of the expression of antioxidant genes (Nrf2 and HO-1). Moreover, PDG exerted notable anti-inflammatory effects via the lessening of interleukin-1 beta, tumor necrosis factor-alpha, cyclooxygenase-2, nuclear factor kappa B, and decreases in the gene expression of inducible nitric oxide synthase. In addition, noteworthy decreases in pro-apoptotic (Bax and caspase-3) levels and increases in anti-apoptotic (Bcl-2) biomarkers suggested an anti-apoptotic effect of PDG. In support, the hippocampal histological examination validated the aforementioned changes. To summarize, the promising neuromodulatory, antioxidative, anti-inflammatory, and anti-apoptotic activities of PDG establish it as a potent therapeutic option for AD.

ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus

Amidst rising cases of antimicrobial resistance, antimicrobial peptides (AMPs) are regarded as a promising alternative to traditional antibiotics. Even so, poor pharmacokinetic profiles of certain AMPs impede their utility necessitating, a careful assessment of potential AMPs' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties during novel lead exploration. Accordingly, the present study utilized ADMET scores to profile seven previously isolated African catfish antimicrobial peptides (ACAPs). After profiling, the peptides were docked against approved bacterial protein targets to gain insight into their possible mode of action. Promising ACAPs were then chemically synthesized, and their antibacterial activity was validated in vitro utilizing the broth dilution method. All seven examined antimicrobial peptides passed the ADMET screening, with two (ACAP-IV and ACAP-V) exhibiting the best ADMET profile scores. The ACAP-V had a higher average binding energy (-8.47 kcal/mol) and average global energy (-70.78 kcal/mol) compared to ACAP-IV (-7.60 kcal/mol and -57.53 kcal/mol), with the potential to penetrate and disrupt bacterial cell membrane (PDB Id: 2w6d). Conversely, ACAP-IV peptide had higher antibacterial activity against E. coli and S. aureus (Minimum Inhibitory Concentration, 520.7 ± 104.3 μg/ml and 1666.7 ± 416.7 μg/ml, respectively) compared to ACAP-V. Collectively, the two antimicrobial peptides (ACAP-IV and ACAP-V) are potential novel leads for the food, cosmetic and pharmaceutical industries. Future research is recommended to optimize the expression of such peptides in biological systems for extended evaluation.

Peptidomics-based identification of an antimicrobial peptide derived from goat milk fermented by Lactobacillus rhamnosus (C25)

Antimicrobial peptides (AMPs) are emerging as promising novel drug applicants. In the present study, goat milk was fermented using Lactobacillus rhamnosus C25 to generate bioactive peptides (BAPs). The peptide fractions generated were separated using ultrafiltration membranes with molecular weight cut-offs of 3, 5, and 10 kDa, and their antimicrobial activity toward Gram-positive and Gram-negative bacteria was investigated. Isolated AMPs were characterized using RP-HPLC and identified by LC-MS/MS. A total of 569 sequences of peptides were identified by mass spectrometry. Out of the 569, 36 were predicted as AMPs, 21 were predicted as cationic, and out of 21, 6 AMPs were helical peptides. In silico analysis indicated that the majority of peptides were antimicrobial and cationic in nature, an important factor for peptide interaction with the negative charge membrane of bacteria. The results showed that the peptides of <5 kDa exhibited maximum antibacterial activity against E. faecalis, E. coli, and S. typhi. Further, molecular docking was used to evaluate the potent MurD ligase inhibitors. On the basis of ligand binding energy, six predicted AMPs were selected and then analyzed by AutoDock tools. Among the six AMPs, peptides IGHFKLIFSLLRV (-7.5 kcal/mol) and KSFCPAPVAPPPPT (-7.6 kcal/mol), were predicted as a high-potent antimicrobial. Based on these findings, in silico investigations reveal that proteins of goat milk are a potential source of AMPs. This is for the first time that the antimicrobial peptides produced by Lactobacillus rhamnosus (C25) fermentation of goat milk have been identified via LC-MS/MS and predicted as AMPs, cationic charges, helical structure in nature, and potent MurD ligase inhibitors. These peptides can be synthesized and improved for use as antimicrobial agents. PRACTICAL APPLICATIONS: Goat milk is considered a high-quality source of milk protein. According to this study, goat milk protein is a potential source of AMPs, Fermentation can yield goat milk-derived peptides with a broad antibacterial activity spectrum at a low cost. The approach described here could be beneficial in that the significant AMPs can be synthesized and used in the pharmaceutical and food industries.

Optimization of Selective Hydrolysis of Cruciferins for Production of Potent Mineral Chelating Peptides and Napins Purification to Valorize Total Rapeseed Meal Proteins

Preventing oxidation and microbial spoilage are both major concerns in food industries. In this context, this study aimed to valorize the total rapeseed meal proteins with controlled enzymatic proteolysis to generate potent mineral-chelating peptides from cruciferins while keeping intact the antimicrobial napins. Implementation of proteolysis of total rapeseed protein isolate with the Prolyve® enzyme highlighted an interesting selective hydrolysis of the cruciferins. Hence, the mechanism of this particular hydrolysis was investigated through a Design of Experiments method to obtain a model for the prediction of kinetics (cruciferin degradation and napin purity) according to the operating conditions applied. Then, multicriteria optimization was implemented to maximize the napin purity and yield while minimizing both enzymatic cost and reaction time. Antioxidant assays of the peptide fraction obtained under the optimal conditions proved the high metal-chelating activity preservation (EC50 = 247 ± 27 µg) for more than three times faster production. This fraction might counteract lipid oxidation or serve as preventing agents for micronutrient deficiencies, and the resulting purified napins may have applications in food safety against microbial contamination. These results can greatly help the development of rapeseed meal applications in food industries.

Antimicrobial bioactive peptides from goat Milk proteins: In silico prediction and analysis

The main goal of this study was to assess the potential proteins of goat milk (i.e. α-s1-casein, α-s2-casein, β-casein, κ-casein, α-lactoglobulin and β-lactalbumin) as precursors of antimicrobial peptides (AMPs). Bioinformatics tools such as BIOPEP-UWM (enzyme action) were used for the in silico gastrointestinal digestion via a cocktail of pepsin, trypsin, and chymotrypsin A. The antimicrobial activity of peptides was predicted by using four algorithms, including Random Forest, Support Vector Machines, Artificial Neural Network and Discriminant Analysis on CAMPR3 online server, which works on Hidden Markov Models. Different online tools predicted the physiochemical properties, allergenicity, and toxicity of peptides as well. In silico gastrointestinal digestion simulation of proteins by enzymes cocktail yielded a total of 83 potential AMPs, with thirteen peptides being confident by all four algorithms. More AMPs were released from β-casein (21) than from β-lactoglobulin (16), α-s1-casein (15), α-s2-casein (12), κ-casein (11) and α-lactalbumin (9). A total of 17 peptides were cationic, and the majority of the peptides were extended AMPs. These peptides were released from α-s1-casein (SGK, IQK), α-s2-casein (SIR, AIH, TQPK), β-casein (GPVR, AVPQR, AIAR, GVPK, SQPK, PVPQK, IH, VPK), k-casein (AIPPK, QQR, IAK, TVPAK). All of the AMPs were anticipated to be non-toxic, and 54 of the 83 peptides were confirmed to be non-allergic, with the remaining 29 suspected of being allergenic and 31 to be predicted to have good water solubility. Further the molecular docking was used to evaluate the potent dihydropteroate synthase (DHPS) inhibitors. On the basis of ligand binding energy, 17 predicted AMPs were selected and then analyzed by AutoDock tools. Among the 17 AMPs, 3 AMPs were predicted as high-potent antimicrobial. Based on these findings, in silico investigations reveal that proteins of goat milk are a potential source of AMPs. These peptides can be synthesized and improved for use in the food sector. PRACTICAL APPLICATIONS: Goat milk is regarded as a high-quality milk protein source. According to this study, goat milk protein is a possible source of AMPs, and therefore, most important AMPs can be synthesized and developed for use in the food sector.

Anticholinesterase Inhibition, Drug-Likeness Assessment, and Molecular Docking Evaluation of Milk Protein-Derived Opioid Peptides for the Control of Alzheimer’s Disease

The drug-likeness and pharmacokinetic properties of 23 dairy-protein-derived opioid peptides were studied using SwissADME and ADMETlab in silico tools. All the opioid peptides had poor drug-like properties based on violations of Lipinski’s rule-of-five. Moreover, prediction of their pharmacokinetic properties showed that the peptides had poor intestinal absorption and bioavailability. Following this, two well-known opioid peptides (βb-casomorphin-5, βb-casomorphin-7) from A1 bovine milk and caffeine (positive control) were selected for in silico molecular docking and in vitro inhibition study with two cholinesterase enzyme receptors important for the pathogenesis of Alzheimer’s disease. Both peptides showed higher binding free energies and inhibitory activities to butyrylcholinesterase (BChE) than caffeine, but in vitro binding energy values were lower than those from the docking model. Moreover, the two casomorphins had lower inhibitory properties against acetylcholinesterase (AChE) than caffeine, although the docking model predicted the opposite. At 1 mg/mL concentrations, βb-casomorphin-5 and βb-casomorphin-7 showed promising results in inhibiting both cholinesterases (i.e., respectively 34% and 43% inhibition of AChE, and 67% and 81% inhibition of BChE). These dairy-derived opioid peptides have the potential to treat Alzheimer’s disease via cholinesterase inhibition. However, appropriate derivatization may be required to improve their poor predicted intestinal absorption and bioavailability.

Effect of rapeseed meal degraded by enzymolysis and fermentation on the growth performance, nutrient digestibility and health status of broilers

The purpose of this study is to investigate the nutritional changes of degraded rapeseed meal and its effects on growth performance, nutrient digestibility and health status of broilers. Raw rapeseed meal (CON), degraded by enzymolysis (protease, ERM), fermentation (Bacillus subtilis, FRM) or both (DRM) were included in diets at 25% and fed to 480 yellow-feathered broilers at 22-63 d of age. Results showed that rapeseed peptide contents (≤1 kDa) were increased (p < 0.05) from 4.13% (CON) to 35.5% (ERM), 24.1% (FRM) and 50.4% (DRM); glucosinolate and erucic acid in DRM were decreased (p < 0.05) by 71.6% and 86.2%, respectively, compared to CON. There were increases (p ≤ 0.029) in feed intake, body weight gain, feed efficiency and precaecal digestibility of dry matter, crude protein, methionine, isoleucine, leucine, lysine, cysteine, phenylalanine, tyrosine, threonine, tryptophan and valine in the three degraded diets. Also, serum immunoglobulin (Ig) A, IgG, glutathione peroxidase, superoxide dismutase and catalase were raised (p ≤ 0.034) in the degraded diets. Additionally, DRM showed more pronounced effects (p < 0.05) on variables related to growth, digestibility and health than ERM and FRM. It is concluded that rapeseed meal degraded by both enzymolysis and fermentation can increase its nutritional values and application in broilers.

Efficient Synthesis of 2-Aminopyridine Derivatives: Antibacterial Activity Assessment and Molecular Docking Studies

A new and suitable multicomponent one-pot reaction was developed for the synthesis of 2-amino-3-cyanopyridine derivatives.

BACKGROUND

This synthesis was demonstrated by the efficient and easy access to a variety of substituted 2-aminopyridines using enaminones as key precursors under solvent-free conditions.

METHODS

A range of spectroscopic techniques was used to determine and confirm the chemical structures (FTIR, 1H NMR, 13C NMR). The antimicrobial potency of synthesized compounds (2a-d) was tested using disk diffusion assays, and the Minimum Inhibitory Concentration (MIC) for the active compounds was determined against a panel of microorganisms, including Gram-positive and Gram-negative bacteria and yeasts. Moreover, a docking analysis was conducted by Molecular Operating Environment (MOE) software to provide supplementary information about the potential, as well as an ADME-T prediction to describe the pharmacokinetic properties of the best compound and its toxicity.

RESULTS

The results of the antimicrobial activity indicated that compound 2c showed the highest activity against Gram-positive bacteria, particularly S. aureus and B. subtilis whose MIC values were 0.039 ± 0.000 µg·mL-1. The results of the theoretical study of compound 2c were in line with the experimental data and exhibited excellent antibacterial potential.

CONCLUSIONS

On the basis of the obtained results, compound 2c can be used as an antibacterial agent model with high antibacterial potency.

In Silico Analysis and Functional Characterization of Antimicrobial and Insecticidal Vicilin from Moth Bean (Vigna aconitifolia (Jacq.) Marechal) Seeds

Vicilin has nutraceutical potential and different noteworthy medicative health-promoting biotic diversions, and it is remarkable against pathogenic microorganisms and insects. In this study, Vigna aconitifolia vicilin (VacV) has been identified and characterized from the seed of Vigna aconitifolia (Jacq.) Marechal (Moth beans). LC-MS/MS analysis of VacV provided seven random fragmented sequences comprising 238 residues, showing significant homology with already reported Vigna radiata vicilin (VraV). VacV was purified using ammonium sulfate precipitation (60%) followed by size exclusion chromatography on Hi-Load 16/60 Superdex 200 pg column and anion-exchange chromatography (Hi trap Q FF column). Purified VacV showed a major ~50 kDa band and multiple lower bands on 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) under both reduced and non-reduced conditions. After all, a three-dimensional molecular structure of VacV was predicted, which showed β-sheeted molecular conformation similar to crystallographic structure of VraV. All Vicilins from V. aconitifolia and other plants were divided into six sub-groups by phylogenetic analysis, and VacV shared a high degree of similarity with vicilins of Vigna radiata, Pisum sativum, Lupinus albus, Cicer arietinum and Glycine max. Additionally, VacV (20 μg) has significant growth inhibition against different pathogenic bacteria along strong antifungal activity (50 μg). Likewise, VacV (3.0 mg) produced significant growth reduction in Rice Weevil Sitophilus oryzae larvae after 9 days compared with control. Furthermore, by using MMT assay, the cytotoxicity effect of VacV on the growth of HepG2 liver cancerous cells was tested. VacV showed cytotoxicity against the HepG-2 line and the acquired value was 180 µg after 48 h. Finally, we performed molecular docking against caspase-3 protein (PDB ID: 3DEI) for VacV bioactive receptor interface residues. Hence, our results reveal that VacV, has nutraceutical potential and moth beans can be used as a rich resource of functional foods.

Proteome-Wide Response of Dormant Caryopses of the Weed, Avena fatua, After Colonization by a Seed-Decay Isolate of Fusarium avenaceum

Promoting seed decay is an ecological approach to reducing weed persistence in the soil seedbank. Previous work demonstrated that Fusarium avenaceum F.a.1 decays dormant Avena fatua (wild oat) caryopses and induces several defense enzyme activities in vitro. The objectives of this study were to obtain a global perspective of proteins expressed after F.a.1-caryopsis colonization by conducting proteomic evaluations on (i) leachates, soluble extrinsic (seed-surface) proteins released upon washing caryopses in buffer and (ii) proteins extracted from whole caryopses; interactions with aluminum (Al) were also evaluated in the latter study because soil acidification and associated metal toxicity are growing problems. Of the 119 leachate proteins classified as defense/stress, 80 were induced or repressed. Defense/stress proteins were far more abundant in A. fatua (35%) than in F.a.1 (12%). Avena defense/stress proteins were also the most highly regulated category, with 30% induced and 35% repressed by F.a.1. Antifungal proteins represented 36% of Avena defense proteins and were the most highly regulated, with 36% induced and 37% repressed by F.a.1. These results implicate selective regulation of Avena defense proteins by F.a.1. Fusarium proteins were also highly abundant in the leachates, with 10% related to pathogenicity, 45% of which were associated with host cell wall degradation. In whole caryopsis extracts, fungal colonization generally resulted in induction of a similar set of Avena proteins in the presence and absence of Al. Results advance the hypothesis that seed decay pathogens elicit intricate and dynamic biochemical responses in dormant seeds.

Analgesic, anti-inflammatory and NF-κB inhibitory activity of aerial parts of Cestrum diurnum

Background

Cestrum diurnum L. (Solanaceae), locally known as buno-Hasnahena, is widely used in different traditional medicinal practices to treat pain, burn, swelling and related disorders. Adequate evidence is not available to support its medicinal properties for further use and drug development. Present study was designed to evaluate its traditional use in pain and inflammation with further characterisation of its chemical constituents through liquid chromatography-mass spectroscopic (LC-MS) analysis.

Methods

Antinociceptive and analgesic potential of methanol extract of the aerial parts of C. diurnum was carried out using carrageenan induced paw oedema and formalin induced paw licking test in mice at the oral doses of 150 and 300 mg/kg body weight. Inhibition of the inflammatory mediator nuclear factor kappa B (NF-κB) was evaluated by tumour necrosis factor α (TNF-α) induced NF-κB activation assay in macrophage cells at the concentration of 100 μg/ml. LC-MS analysis of the extract was performed to characterise the active component responsible for bioactivities.

Results

The extract significantly inhibited (p < 0.05) carrageenan induced paw oedema at both doses tested and the effect persisted throughout the entire experimental period of 3 h with the highest activity (50% inhibition) observed at 3rd h. Further, the extract significantly inhibited (p < 0.05) formalin induced paw licking both in the early and late phase at the aforementioned dose levels. The extract also downregulated the expression of NF-κB p65 protein in the TNF-α induced NF-κB activation assay. LC-MS analysis of the extract indicated the presence of some important secondary metabolites including nicotine, nornicotine, ursolic acid, vitamin D3 and its derivatives.

Conclusions

The results of this study supported the folkloric uses of the plant in pain and inflammations. The insights and observations suggest the action might involve downregulation of NF-κB p65 protein expression and/or inhibition of autacoids (histamine, serotonin, prostaglandin).

sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks

Short antimicrobial peptides (sAMPs) belong to a significant repertoire of antimicrobial agents and are known to possess enhanced antimicrobial activity, higher stability and less toxicity to human cells, as well as less complex than other large biological drugs. As these molecules are significantly important, herein, a prediction method for sAMPs (with a sequence length ≤ 30 residues) is proposed for accurate and efficient prediction of sAMPs instead of laborious and costly experimental approaches. Benchmark dataset was collected from a recently reported study and sequences were converted into three channel images comprising information related to the position, frequency and sum of 12 physiochemical features as the first, second and third channels, respectively. Two image-based deep neural networks (DNNs), i.e. RESNET-50 and VGG-16 were trained and evaluated using various metrics while a comparative analysis with previous techniques was also performed. Validation of sAMP-PFPDeep was also performed by using molecular docking based analysis. The results showed that VGG-16 provided more accurate results, i.e. 98.30% training accuracy and 87.37% testing accuracy for predicting sAMPs as compared to those of RESNET-50 having 96.14% training accuracy and 83.87% testing accuracy. However, the comparative analysis revealed that both these models outperformed previously reported state-of-the-art methods. Based on the results, it is concluded that sAMP-PFPDeep can help identify antimicrobial peptides with promising accuracy and efficiency. It can help biologists and scientists to identify antimicrobial peptides, by further aiding the computer-aided drug design and discovery, as well as virtual screening protocols against various pathologies. sAMP-PFPDeep is available at (https://github.com/WaqarHusain/sAMP-PFPDeep).

Biochemical and in silico study of leaf and bark extracts from Aphanamixis polystachya against common pathogenic bacteria

Aphanamixis polystachya may be a natural, renewable resource against antibiotic-resistant bacterial infections. The antibacterial activity of A. polystachya leaf and bark extracts was investigated against three antibiotic-resistant bacterial species and one fungus. Methanolic leaf extract showed only limited antibacterial activity but both methanolic and aqueous bark extract showed high antimicrobial activity. In an antioxidant activity test, leaf and bark extracts exhibited 50% free radical scavenging at a concentration of 107.14 ± 3.14 μg/mL and 97.13 ± 3.05 μg/mL, respectively, indicating that bark extracts offer more antioxidative activity than leaf extracts. Bark extracts also showed lower toxicity than leaf extracts. This suggests that bark extracts may offer greater development potential than leaf extracts. The molecular dynamics were also investigated through the simulated exploration of multiple potential interactions to understand the interaction dynamics (root-mean-square deviation, solvent-accessible surface area, radius of gyration, and the hydrogen bonding of chosen compounds to protein targets) and possible mechanisms of inhibition. This molecular modeling of compounds derived from A. polystachya revealed that inhibition may occur by binding to the active sites of the target proteins of the tested bacterial strains. A. polystachya bark extract may be used as a natural source of drugs to control antibiotic-resistant bacteria.

Structural and Functional Annotation of Napin-Like Protein from Momordica charantia to Explore its Medicinal Importance

Seed storage proteins not just provide essential nutritional ingredients for growth of seedlings but also have their potential role in defense mechanisms of plants. Napin is a seed storage protein and belongs to 2S albumin family. Napin and napin-like protein have many biological defensive activities including antifungal, antimicrobial, trypsin inhibitor, and also act as antagonist of calmodulin. Napin protein possesses various isoforms with different biological activities. In this study, the protein sequence of napin from Momordica charantia was retrieved from GenPept database for characterization. A complete annotation of napin including its physicochemical properties was done. Three dimensional (3D) modeling and interactions of napin-like protein with other proteins were also predicted using various bioinformatics tools. A phylogram of napin-like protein from M. charantia with its homologs was also reconstructed to reveal its evolutionary relationships with napins and other 2S albumin proteins from various plants. The study has revealed the structural characterization, biological interactions, and evolutionary background which will play crucial role in exploring the medicinal and biological potentials of napin-like protein from M. charantia as well as worth of napin and napin-like protein has been disclosed.

Synergistic anti-cancer action of salicylic acid and cisplatin on HeLa cells elucidated by network pharmacology and in vitro analysis

AIM

To investigate the anti-cancer potential of salicylic acid and cisplatin combination in HeLa cells and the underlying mechanism.

MAIN METHODS

Drugs and disease targets were extracted from DrugBank, BATMAN-TCM, STITCH, PharmMapper and Comparative Toxigenomics Database. Cytoscape 3.8.2 was used to merge the protein-protein interaction networks and select core targets. GO and KEGG analysis was done using Metascape and WebGestalt. Effect of salicylic acid and cisplatin alone and in combination on cells viability was studied by MTT assay. The type of interaction between salicylic acid and cisplatin was determined by CompuSyn. Apoptosis was evaluated by molecular docking, Rhodamine-123, DAPI, AO/EtBr staining, flow cytometry, qRT-PCR and western blotting. Metastasis was studied using scratch assay and western blotting. UHRF1 transient silencing was performed by siRNA.

KEY FINDINGS

Out of 420, 1863 and 1362 respective targets of salicylic acid, cisplatin and cervical cancer, 18 core proteins were enriched in apoptosis and cell migration related pathways. IC50 value of cisplatin was reduced by 14 fold in combination with salicylic acid at IC20 (4 μM). There was loss of mitochondrial membrane potential and downregulation of UHRF1, pAkt, full length PARP and pro-caspase 3 expression. Transient silencing of UHRF1 also induced mitochondrial depolarization and apoptosis. The combination also exhibited anti-metastasis effect as it suppressed migration, upregulated PAX1 and downregulated MMP-2.

SIGNIFICANCE

Reduction in cisplatin concentration, enhanced anti-cancer effects and UHRF1 downregulation due to synergistic interaction between salicylic acid and cisplatin underscores the therapeutic importance of the combination to overcome chemo-resistance and side effects of cisplatin.

Prediction and analysis of antimicrobial peptides from rapeseed protein using in silico approach

The purpose of this study was to evaluate the potential of rapeseed proteins including Napin, Cruciferin, and Oleosin as precursors of antimicrobial peptides (AMPs), and to investigate physicochemical properties, secondary structures, toxicity, and allergenicity of AMPs using several bioinformatics tools such as BIOPEP, CAMP, APD, SOPMA, ToxinPred, and AllergenFP. A total of 26 novel AMPs were obtained by in silico hydrolysis using nine proteases, and six peptides were tested positive by all the four algorithms including Random Forest (RF), Support Vector Machines (SVM), Artificial Neural Network (ANN), and Discriminant Analysis (DA). More AMPs were generated from Cruciferin than from Napin and Oleosin. Trypsin was the most effective enzyme for AMPs production compared with other used proteases. About two-third of peptides were cationic. Interestingly, most peptides were extended AMPs. All AMPs were predicted to be non-toxic, and 14 peptides were non-allergenic. These results indicate that rapeseed protein is a good potential source of AMPs as demonstrated by in silico analyses and the theoretical knowledge obtained provides a basis for further development and production of rapeseed AMPs. PRACTICAL APPLICATIONS: Rapeseed protein is a high-quality plant protein resource. However, it is usually used as animal feed or fertilizer. Effective enzymatic hydrolysis of rapeseed protein can release bioactive peptides and improve the utilization value. This study indicates that rapeseed protein is a good potential source of AMPs as demonstrated by in silico analyses. The theoretical knowledge obtained provides a basis for further development and production of rapeseed AMPs.