Search Results (708)

Sindbis virus (SINV), a prototype of the Alphavirus genus (family Togaviridae), is a globally distributed arbovirus causing febrile rash and debilitating arthritis in humans. Viral structural proteins—capsid (C), E1, and E2—are fundamental to the virion’s architecture, mediating all stages from assembly to host cell entry and pathogenesis, thus representing critical targets for study. This review consolidates the historical and current understanding of SINV structural biology, tracing progress from early microscopy to recent high-resolution cryo-electron microscopy (cryo-EM) and X-ray crystallography. We detail the virion’s precise T = 4 icosahedral architecture, composed of a nucleocapsid core and an outer glycoprotein shell. Key functional roles tied to protein structure are examined: the capsid’s dual capacity as a serine protease and an RNA-packaging scaffold that interacts with the E2 cytoplasmic tail; the E1 glycoprotein’s function as a class II fusion protein driving membrane fusion; and the E2 glycoprotein’s primary role in receptor binding, which dictates cellular tropism and serves as the main antigenic target. Furthermore, we connect these molecular structures to viral evolution and disease, analyzing how genetic variation among SINV genotypes, particularly in the E2 gene, influences host adaptation, immune evasion, and the clinical expression of arthritogenic and neurovirulent disease. In conclusion, the wealth of structural data on SINV offers a powerful paradigm for understanding alphavirus biology. However, critical gaps persist, including the high-resolution visualization of dynamic conformational states during viral entry and the specific molecular determinants of chronic disease. Addressing these challenges through integrative structural and functional studies is paramount. Such knowledge will be indispensable for the rational design of next-generation antiviral therapies and broadly protective vaccines against the ongoing threat posed by SINV and related pathogenic alphaviruses. Full article

The SARS-CoV-2 main protease (M^pro) is a well-established target for antiviral drug development One such inhibitor, nirmatrelvir, in combination with ritonavir as a booster, has already been introduced into the market, under the name Paxlovid. However, being an RNA virus, SARS-CoV-2 is prone to the emergence of resistance mutations. A number of such mutations have been characterized, although they have not yet been shown to play a significant role in clinical settings; these include S144A, E166V, H172Y, and Q189K. We recombinantly produced these mutants and studied the corresponding proteins using X-ray crystallography, enzymology, and biophysical approaches. We discuss the potential of each mutant to lead to a widespread nirmatrelvir resistance scenario. We also demonstrate that one of our own inhibitors (13b-K), while showing some degree of cross-resistance with nirmatrelvir, exhibits much higher inhibitory activity against the M^pro carrying the E166V mutation. Full article

The use of exogenous enzymes in the nutrition of dairy cows is an innovative and efficient strategy to maximize productivity and milk quality, with positive applications in the economic and environmental aspects of dairy farming. Therefore, the objective of this study was to evaluate whether the addition of a blend of exogenous enzymes to the diet of lactating Jersey cows has a positive effect on productive performance, milk quality, animal health, ruminal environment, and digestibility. Twenty-one primiparous Jersey cows, with 210 days in lactation (DL), were used. The exogenous enzymes used were blends containing mainly protease, in addition to cellulase, xylanase, and beta-glucanase. The animals were divided into three groups with seven replicates per group (each animal being the experimental unit), as follows: Control (T-0), basal diet without enzyme addition; Treatment (T-80), animals fed enzymes in the diet at a daily dose of 80 mg per kg of dry matter (DM); Treatment (T-160), animals fed enzymes in the diet at a daily dose of 160 mg per kg of DM. The study lasted 84 days, during which higher milk production was observed in the treated groups (T-80 and T-160) compared to the control group (p = 0.04). When calculating feed efficiency from days 1 to 84, greater efficiency was observed in both groups that received the blend compared to the control (p = 0.05). In the centesimal composition of the milk, it was observed that the percentage of protein in the milk of the T-160 group was higher compared to the control group (p = 0.03). The effect of the enzymes was verified for butyric (p = 0.05) and palmitic (p = 0.05) fatty acids. We also observed the effect of the enzyme blend on the amount of volatile fatty acids (VFAs), which were higher in the ruminal fluid of cows that received the enzymes (p = 0.01). Cows that consumed enzymes showed a higher apparent digestibility coefficient of crude protein (p = 0.01). In vitro, the main result is related to lower gas production in 24 and 48 h at T-160. We concluded that the use of a blend of exogenous enzymes in the diet of lactating Jersey cows was able to increase milk production in these animals, resulting in greater feed efficiency and also an increase in milk protein content, positively modulating the fatty acid profile in the rumen and improving the apparent digestibility of nutrients. Full article

Despite the widespread use of vaccines against SARS-CoV-2, COVID-19 continues to pose global health challenges, requiring efficient drug screening and repurposing strategies. This study presents a novel hybrid framework that integrates deep learning (DL) with molecular docking to accelerate the identification of potential therapeutics. The framework comprises three crucial steps: (1) a previously developed DL model is employed to rapidly screen candidate compounds, selecting those with predicted interaction scores above a cut-off value of 0.8; (2) AutoDock Vina version 1.5.6 and LeDock version 1.0 are used to evaluate binding affinities, with a threshold of <−7.0 kcal·mol⁻¹; and (3) predicted drug–protein binding sites are evaluated to determine their overlap with known active residues of the target protein. We first validated the framework using four experimentally confirmed COVID-19 drug–target pairs and then applied it to identify potential inhibitors of the SARS-CoV-2 main protease (M^Pro). Among 29 drug candidates selected based on antiviral, anti-inflammatory, or anti-cancer properties, only Enasidenib met all three selection criteria, showing promise as an M^Pro inhibitor. However, further experimental and clinical studies are required to confirm its efficacy against SARS-CoV-2. This work provides an interpretable strategy for virtual screening and drug repurposing, which can be readily adapted to other DL models and docking tools. Full article

Background: There is growing evidence suggesting that SARS-CoV-2 may contribute to metabolic dysfunction. SARS-CoV-2 infection is associated with systemic inflammation, oxidative stress, and metabolic dysregulation, all of which may impair liver function and promote glucose intolerance. This study investigated the role of SARS-CoV-2, specifically its Main Protease (M^pro), in accelerating insulin resistance and metabolic dysfunction in HepG2 cells in vitro. Methods: HepG2 cells were treated with varying concentrations of M^pro (2.5, 5, 10, 20, 40, 80, and 160 nmol/mL) for 24 h to assess cytotoxicity and glucose uptake. Based on initial findings, subsequent assays focused on higher concentrations (40, 80, and 160 nmol/mL). The effects of M^pro on cell viability, protein kinase B (AKT) expression, matrix metallopeptidase-1 (MMP1), dipeptidyl peptidase 4 (DPP4), interleukin-6 (IL-6) expression, and lipid peroxidation were investigated. Results: Our findings reveal that the SARS-CoV-2 M^pro treatment led to a concentration-dependent reduction in glucose uptake in HepG2 cells. Additionally, the M^pro treatment was associated with reduced insulin-stimulated AKT activation, particularly at higher concentrations. Inflammatory markers such as IL-6 were elevated in the extracellular medium, while DPP4 expression was decreased. However, extracellular soluble DPP4 (sDPP4) levels did not show a significant change. Despite these changes, cell viability remained relatively unaffected, suggesting that the HepG2 cells were able to maintain overall metabolic functions under M^pro exposure. Conclusions: This study demonstrated the concentration-dependent impairment of hepatic glucose metabolism, insulin signaling, and inflammatory pathways in HepG2 cells acutely exposed to the SARS-CoV-2 M^pro. These findings warrant further investigation to explore the long-term metabolic effects of SARS-CoV-2 and its proteases in the liver and to develop potential therapeutic approaches for post-viral metabolic complications. Full article

AAA+ ATPases are ring-shaped hexameric protein complexes that operate as elaborate macromolecular motors, driving a variety of ATP-dependent cellular processes. AAA+ ATPases undergo large-scale conformational changes that lead to the conversion of chemical energy from ATP into mechanical work to perform a wide range of functions, such as unfolding and translocation of the protein substrate inside a proteolysis chamber of an AAA+-associated protease. Despite extensive biochemical studies on these macromolecular assemblies, the mechanism of substrate unfolding and degradation has long remained elusive. Indeed, until recently, structural characterization of AAA+ protease complexes remained hampered by the size and complexity of the machinery, harboring multiple protein subunits acting together to process proteins to be degraded. Additionally, the major structural rearrangements involved in the mechanism of this complex represent a crucial challenge for structural biology. Here, we report the main advances in deciphering molecular details of the proteolytic reaction performed by AAA+ proteases, based on the remarkable progress in structural biology techniques. Particular emphasis is placed on the latest findings from high-resolution structural analysis of the ClpXP proteolytic complex, using crystallographic and cryo-EM investigations. In addition, this review presents some additional dynamic information obtained using solution-state NMR. This information provides molecular details that help to explain the protein degradation process by such molecular machines. Full article

Solid-state fermentation (SSF) involves the growth of microorganisms on solid substrates, mimicking natural environments of many species. Due to sustainability concerns, transforming agro-industrial by-products into value-added products through SSF has been increasingly studied. Brewer’s spent grain (BSG), the main by-product of beer production, mostly consists of barley grain husks, making BSG a great support for microorganism cultivation. Although autoclaving remains the standard sterilization and pretreatment method of substrates, electric field technologies and their attendant ohmic heating (OH) have great potential as an alternative technology. In the present work, pretreatment of BSG by OH was explored in SSF with Aspergillus niger to produce commercially valuable enzymes. OH favored the solubilization of phenolic compounds, total protein, and reducing sugars significantly higher than autoclaving. SSF of treated BSG led to the production of lignocellulosic enzymes, with xylanases being the most active, reaching 540 U/g, a 1.5-fold increase in activity compared to autoclaved BSG. Protease activity was also improved 1.6-fold by OH, resulting in 49 U/g. Our findings suggest that OH treatment is an effective alternative to autoclaving and that its integration with SSF is a sustainable strategy to enhance by-product valorization through enzyme production with many industrial applications, according to circular economy guidelines. Full article

The global impact of the COVID-19 crisis has underscored the need for novel therapeutic candidates capable of efficiently targeting essential viral proteins. Existing therapeutic strategies continue to encounter limitations such as reduced efficacy against emerging variants, safety concerns, and suboptimal pharmacodynamics, which emphasize the potential of natural-origin compounds as supportive agents with immunomodulatory, anti-inflammatory, and antioxidant benefits. The present study significantly advances prior molecular docking research through comprehensive virtual screening of structurally related analogs derived from antiviral phytochemicals. These compounds were evaluated specifically against the SARS-CoV-2 main protease (3CLpro) and papain-like protease (PLpro). Utilizing chemical similarity algorithms via the ChEMBL database, over 600 candidate molecules were retrieved and subjected to automated docking, interaction pattern analysis, and comprehensive ADMET profiling. Several analogs showed enhanced binding scores relative to their parent scaffolds, with CHEMBL1720210 (a shogaol-derived analog) demonstrating strong interaction with PLpro (−9.34 kcal/mol), and CHEMBL1495225 (a 6-gingerol derivative) showing high affinity for 3CLpro (−8.04 kcal/mol). Molecular interaction analysis revealed that CHEMBL1720210 forms hydrogen bonds with key PLpro residues including GLY163, LEU162, GLN269, TYR265, and TYR273, complemented by hydrophobic interactions with TYR268 and PRO248. CHEMBL1495225 establishes multiple hydrogen bonds with the 3CLpro residues ASP197, ARG131, TYR239, LEU272, and GLY195, along with hydrophobic contacts with LEU287. Gene expression predictions via DIGEP-Pred indicated that the top-ranked compounds could influence biological pathways linked to inflammation and oxidative stress, processes implicated in COVID-19’s pathology. Notably, CHEMBL4069090 emerged as a lead compound with favorable drug-likeness and predicted binding to PLpro. Overall, the applied in silico framework facilitated the rational prioritization of bioactive analogs with promising pharmacological profiles, supporting their advancement toward experimental validation and therapeutic exploration against SARS-CoV-2. Full article

The insect resistance expression of Bacillus thuringiensis (Bt) cotton (Gossypium hirsutum L.) is unstable due to temporal and spatial variations in the Bt protein content in different organs and growth stages. The aim of this study was to improve the Bt protein content in cotton flowers and investigate the underlying physiological mechanism using biochemical analytical methods. In this study, a split-plot design with three replications was used. The main plots included two Bt cotton cultivars (a conventional cultivar, Sikang1 (S1), and a hybrid cultivar, Sikang3 (S3)), while five soil nitrogen application levels (CK (control check): normal level; N1: 125% of the CK; N2: 150% of the CK; N3: 175% of the CK; N4: 200% of the CK) constituted the subplots. The Bt protein content and related nitrogen metabolism parameters were measured. We found that the Bt protein content increased and then decreased with increasing nitrogen rates. It reached its maximum at N3, with significant increases of 71.86% in 2021 and 39.36% in 2022 compared to the CK. Correlation analysis indicated that the Bt protein content was significantly positively related to the soluble protein and free amino acid contents, as well as the GPT (glutamic pyruvic transaminase), GOT (glutamic oxaloacetic transaminase), GS (glutamine synthetase) and GOGAT (glutamate synthetase) activities. On the other hand, negative correlations were found between the Bt protein content and protease and peptidase activities. In addition, stepwise regression and path analysis indicated that the increased Bt protein content was mainly due to the enhanced GS and GOGAT activities. In summary, appropriately increasing nitrogen fertilizer application is a practical way to increase flower Bt protein content and insecticidal efficacy of Bt cotton. These findings provide an actionable agronomic strategy for sustaining Bt expression during the critical flowering period. Full article

Background/Objectives: Combination therapies using traditional Chinese medicine and Western drugs have gained attention for their enhanced therapeutic effects and reduced side effects. Toujie Quwen Granules (TQG), known for its antiviral properties, particularly against respiratory viruses, could offer new treatment strategies when combined with antiviral drugs like arbidol, especially for diseases such as Coronavirus disease. This study investigates the synergistic mechanisms between arbidol and components from TQG against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M^pro). Methods: We identified compounds from TQG via existing data. Multi-ligand molecular docking, pharmacokinetic/toxicity screening, and preliminary simulations were performed to assess potential synergistic compounds with arbidol. UPLC-Q-Exactive Orbitrap-MS verified the presence of these compounds. Extended simulations and in vitro assays, including Luciferase and surface plasmon resonance, validated the findings. Results: Five compounds interacted with arbidol in synergy based on docking and preliminary dynamics simulation results. Only Baicalein (HQA004) could be identified in the herbal remedy by untargeted metabolomics, with ideal pharmacokinetic properties, and as a non-toxic compound. Extended simulations revealed that HQA004 enhanced arbidol’s antiviral activity via a “Far” Addition Mechanism #2, with an optimal 2:1 arbidol:HQA004 ratio. The movements of arbidol (diffusion and intramolecular conformational shifts) in the system were significantly reduced by HQA004, which may be the main reason for the synergism that occurred. In vitro experiments confirmed an increased inhibition of M^pro by the combination. Conclusions: HQA004 demonstrated synergistic potential with arbidol in inhibiting M^pro. The development of combination therapies integrating Western and herbal medicine is supported by these findings for effective antiviral treatments. Full article

Soybean flours are widely used as a protein-rich ingredient in fish aquafeeds, and to obtain value-added compounds after a previous treatment with proteases. Additionally, non-starch polysaccharidases (NSPases) enhance dietary protein bioaccessibility and have been used as feed additives. In this study, defatted soybean flour was hydrolyzed using Sparus aurata gastric proteases and varying doses of a commercial blend of acidic NSPases. Reactions occurred at 25 °C for 3 h under typical fish stomach pH conditions (3.5–5.6). We modeled the hydrolytic process using response surface methodology, focusing on the released peptides and carbohydrates. The main finding was the efficient control of the degree of protein hydrolysis. We achieved 6–25% hydrolysis for peptides below 10 kDa by adjusting the carbohydrase dose and reaction pH. This work confirms that acidic commercial NSPases improve soybean flour protein hydrolysis when combined with S. aurata gastric proteases. Full article

The SARS-CoV-2 main protease (Mpro) is a validated therapeutic target for inhibiting viral replication. Few compounds have advanced clinically, underscoring the difficulty in optimizing both target affinity and drug-like properties. To address this challenge, we integrated machine learning (ML), molecular docking, and molecular dynamics (MD) simulations to investigate the balance between pharmacodynamic (PD) and pharmacokinetic (PK) properties in Mpro inhibitor design. We developed ML models to classify Mpro inhibitors based on experimental IC₅₀ data, combining molecular descriptors with structural insights from MD simulations. Our Support Vector Machine (SVM) model achieved strong performance (training accuracy = 0.84, ROC AUC = 0.91; test accuracy = 0.79, ROC AUC = 0.86), while our Logistic Regression model (training accuracy = 0.78, ROC AUC = 0.85; test accuracy = 0.76, ROC AUC = 0.83). Notably, PK descriptors often exhibited opposing trends to binding affinity: hydrophilic features enhanced binding affinity but compromised PK properties, whereas hydrogen bonding, hydrophobic, and π–π interactions in Mpro subsites S2 and S3/S4 are fundamental for binding affinity. Our findings highlight the need for a balanced approach in Mpro inhibitor design, strategically targeting these subsites may balance PD and PK properties. For the first time, we demonstrate antagonistic trends between pharmacokinetic (PK) and pharmacodynamic (PD) features through the integrated application of ML/MD. This study provides a computational framework for rational Mpro inhibitors, combining ML and MD to investigate the complex interplay between enzyme inhibition and drug likeness. These insights may guide the hit-to-lead optimization of the novel next-generation Mpro inhibitors of SARS-CoV-2 with preclinical and clinical potential. Full article

This review presents information obtained over the past 10 years on the methods to control the widespread worldwide phytopathogen Pectobacterium carotovorum subsp. carotovorum (Pcc). This bacterium is among the ten most dangerous phytopathogens; it affects a wide range of cultivated plants: vegetables, ornamental and medicinal crops, both during vegetation and during the storage of fruits. Symptoms of Pcc damage include the wilting of plants, blackening of vessels on leaves, stems and petioles. At the flowering stage, the stem core gradually wilts and, starting from the root, the stem breaks and the plant dies. Pcc is a rod-shaped, non-capsule and endospore-forming facultative anaerobic Gram-negative bacterium with peritrichous flagellation. Pcc synthesizes bacteriocins—carocins. The main virulence factors of Pcc are the synthesis of N-acyl-homoserine lactone (AHL) and plant cell wall-degrading enzymes (PCWDEs) (pectinases, polygalacturonases, cellulases, and proteases). Diagnostic methods for this phytopathogen include polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), multilocus genotyping of strain-specific genes and detection of unique volatile organic compounds (VOCs). The main methods to control this microorganism include the use of various chemicals (acids, phenols, esters, salts, gases), plant extracts (from grasses, shrubs, trees, and algae), antagonistic bacteria (Bacillus, Pseudomonas, Streptomyces, and lactic acid bacteria), viruses (including a mixture of bacteriophages), and nanomaterials based on metals and chitosan. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, remains a major global health threat. The virus enters host cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor. Several small-molecule antiviral drugs, including molnupiravir, favipiravir, remdesivir, and nirmatrelvir have been shown to inhibit SARS-CoV-2 replication and are approved for treating SARS-CoV-2 infections. Nirmatrelvir inhibits the viral main protease (M^pro), a key enzyme for processing polyproteins in viral replication. In contrast, molnupiravir, favipiravir, and remdesivir are prodrugs that target RNA-dependent RNA polymerase (RdRp), which is crucial for genome replication and subgenomic RNA production. However, undergoing extensive metabolism profoundly impacts their therapeutic effects. Carboxylesterases (CES) are a family of enzymes that play an essential role in the metabolism of many drugs, especially prodrugs that require activation through hydrolysis. Molnupiravir is activated by carboxylesterase-2 (CES2), while remdesivir is hydrolytically activated by CES1 but inhibits CES2. Nirmatrelvir and remdesivir are oxidized by the same cytochrome P450 (CYP) enzyme. Additionally, various transporters are involved in the uptake or efflux of these drugs and/or their metabolites. It is well established that drug-metabolizing enzymes and transporters are differentially expressed depending on the cell type, and these genes exhibit significant polymorphisms. In this review, we examine how CES-related cellular and genetic factors influence the therapeutic activities of these widely used COVID-19 medications. This article highlights implications for improving product design, targeted inhibition, and personalized medicine by exploring genetic variations and their impact on drug metabolism and efficacy. Full article

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease of 2019 (COVID-19) and has persistently caused infections since its emergence in late 2019. The main protease (Mpro) of SARS-CoV-2 plays a crucial role in its life-cycle; thus, it is an important target for drug development. One of the first virus-specific drugs that has been approved for the treatment of COVID-19 patients is Paxlovid, which contains nirmatrelvir, a covalent inhibitor of Mpro. Screening of inhibitor candidates and specificity studies also rely on efficient substrates and activity assays. Casein is one of the most commonly applied universal substrates that can be used to study a wide range of proteases, including SARS-CoV-2 Mpro. Casein is a known substrate for Mpro in vitro, but the specific casein isoform cleaved by Mpro remained unidentified, and the cleavage sites have yet to be determined. This work studied cleavage of α-, β- and κ-isoforms of bovine casein by SARS-CoV-2 Mpro, using in vitro and in silico approaches. The candidate cleavage sites were predicted in silico based on the protein sequences, and the cleavage positions were identified based on mass spectrometric analysis of cleavage fragments. Based on our results, only β-casein contains cleavage sites for Mpro and thus can be used as its substrate in vitro. The newly identified cleavage site sequences further widen the knowledge about the specificity of SARS-CoV-2 Mpro. Full article