Search Results (9,234)

Peptides isolated from various biological materials are potential sources for novel angiotensin-converting enzyme (ACE) inhibitors. Here, the ACE-inhibitory activity of peptides derived from papain-digested hydrolysates of porcine liver and placenta were investigated. A high-throughput method was developed to identify potential bioactive peptides from the hydrolysates using in silico enzymatic cleavage, HPLC-MS/MS, and bioinformatics tools. Four peptides (FWG, MFLG, SDPPLVFVG, and FFNDA) were selected based on their predicted bioactivity, then synthesised and tested for ACE inhibition. All samples demonstrated ACE-inhibitory activity, with FWG and MFLG showing greater potency than SDPPLVFVG and FFNDA. The placenta hydrolysate outperformed both the liver hydrolysate and synthetic peptides in ACE inhibition, possibly due to it containing a higher proportion of dipeptides. The synthetic peptides’ IC50 values were comparable to those reported for porcine muscle-derived peptides in previous studies. While less potent than the commercial ACE inhibitor captopril, the identified peptides showed promising ACE-inhibitory activity. This research demonstrates the potential of porcine liver and placenta as sources of novel ACE-inhibitory peptides and highlights the effectiveness of the developed high-throughput method for identifying bioactive peptides; this method could subsequently be adapted to other peptide sources, facilitating the development of innovative functional foods or nutraceuticals. Full article

Houttuynia cordata Thunb. holds a longstanding reputation as a traditional folk remedy in East Asia, where it has been employed to treat a variety of inflammatory conditions, nephritis, hepatitis and cancer. Despite its extensive use, there exists a paucity of research examining its efficacy in managing thyroid disorders and diabetes. Moreover, the bioactive components responsible for modulating the molecular pathways remain elusive. Objectives: This research aimed to determine the key bioactive components in the ethanolic extract of H. cordata Thunb. (HCEE) responsible for its thyroid-modifying properties and examine its effects on rats with experimentally induced hypothyroidism and diabetes. Methods: Molecular docking was performed to investigate the possible mechanisms of thyroid regulation of HCEE constituents. Researchers induced hypothyroidism in rats by adding 6-propyl-2-thiouracil to their drinking water for a period of four weeks. To induce diabetes, the rats received an intraperitoneal injection of streptozotocin. The animals were then given daily oral doses of HCEE (500 mg/kg b.w.), levothyroxine (50 mg/kg b.w.), or glibenclamide (5 mg/kg b.w.) for 28 days. Following this treatment, standard methods were employed to measure biochemical parameters in the rats’ serum. Results: The results demonstrate that HCEE ameliorated hypothyroidism by increasing serum T3 (14.38%) and T4 (125.96%) levels and decreasing TSH (p < 0.01; −41.75%) levels. In diabetic rats with induced hypothyroidism, HCEE significantly (p < 0.001) increased T3 (149.51%) and T4 (73.54%) levels with reduced TSH (−64.39%) levels. In silico analysis demonstrated that the identified bioactive compounds from HCEE may enhance thyroid hormone function through interaction with the thyroid hormone receptor protein TRβ1 (PDB:3GWS), similar to the conventional pharmaceuticals levothyroxine and triiodothyronine (T3). Conclusions: HCEE exhibits potential as a natural alternative to synthetic medications in the prevention and treatment of thyroid dysfunctions. Full article

Enterohemorrhagic Escherichia coli (EHEC) is a significant public health concern due to its ability to form biofilms, enhancing its resistance to antimicrobials and contributing to its persistence in food processing environments. Traditional antibiotics often fail to target these biofilms effectively, leading to increased bacterial resistance. This study aims to explore the efficacy of novel antibiofilm agents, specifically halogenated pyrimidine derivatives, against EHEC. We screened pyrimidine and 31 halogenated pyrimidine derivatives for their antimicrobial and antibiofilm activities against EHEC using biofilm quantification assays, SEM analysis, motility, and curli production assessments. Our findings reveal that certain halogenated pyrimidine derivatives, notably 2-amino-5-bromopyrimidine (2A5BP), 2-amino-4-chloropyrrolo[2,3-d]pyrimidine (2A4CPP), and 2,4-dichloro-5-iodo-7H-pyrrolo[2,3-d]pyrimidine (2,4DC5IPP) at 50 µg/mL, exhibited significant inhibitory effects on EHEC biofilm formation without affecting bacterial growth, suggesting a targeted antibiofilm action. These compounds effectively reduced curli production and EHEC motility, essential factors for biofilm integrity and development. qRT-PCR analysis revealed that two active compounds downregulated the expression of key curli genes (csgA and csgB), leading to reduced bacterial adhesion and biofilm formation. Additionally, in silico ADME–Tox profiles indicated that these compounds exhibit favorable drug-like properties and lower toxicity compared with traditional pyrimidine. This study highlights the potential of halogenated pyrimidine derivatives as effective antibiofilm agents against EHEC, offering a promising strategy for enhancing food safety and controlling EHEC infections. The distinct mechanisms of action of these compounds, particularly in inhibiting biofilm formation and virulence factors without promoting bacterial resistance, underscore their therapeutic potential. Full article

Vitex agnus-castus L., a medicinal plant widespread in the Middle East and Europe, is traditionally used to treat various disorders. In this study, extracts from its leaves, collected in Algeria, were evaluated for their antioxidant, enzymatic, and antibacterial activities through in vitro and in silico studies. The hydroalcoholic extract was fractionated using solvents of varying polarity to isolate bioactive compounds with potential biological effects. Notable levels of total phenolics, flavonoids, and flavonols were detected in the dichloromethane (CH₂Cl₂) and ethyl acetate (EtOAc) extracts. NMR and GC-MS were used to identify metabolites in the extracts, which were discussed in relation to their biological activities. Antioxidant assays showed that the EtOAc extract had a remarkable effect, particularly in the DPPH^• free radicals test (IC₅₀ = 15.68 ± 1.51 μg/mL), while enzymatic assays revealed that the dichloromethane extract moderately inhibited butyrylcholinesterase (IC₅₀ = 133.54 ± 1.45 μg/mL). Antibacterial assays showed that the extracts inhibited the growth of Staphylococcus aureus, Bacillus subtilis, and Escherichia coli strains, with the most significant effect observed for the n-hexane extract, especially against S. aureus and B. subtilis (respectively, 22.33 ± 0.47 and 18.33 ± 0.47 mm diameters). These outcomes were validated via molecular docking simulations on three DNA gyrase enzymes: 3G7E (from E. coli), 3G75 (from S. aureus), and 4DDQ (from B. subtilis), revealing that linolenic and palmitic acids, as well as phytol significantly interacted with these enzymes, showing varying binding affinities and suggesting antibacterial potential against the targeted species E. coli and S. aureus. These findings highlight the potential therapeutic use of V. agnus-castus leaves, encouraging further research into their applicability in the development of plant-derived drugs. Full article

Background/Objectives: Determining appropriate cellular objectives is crucial for the system-scale modeling of biological networks for metabolic engineering, cellular reprogramming, and drug discovery applications. The mathematical representation of metabolic objectives can describe how cells manage limited resources to achieve biological goals within mechanistic and environmental constraints. While rapidly proliferating cells like tumors are often assumed to prioritize biomass production, mammalian cell types can exhibit objectives beyond growth, such as supporting tissue functions, developmental processes, and redox homeostasis. Methods: This review addresses the challenge of determining metabolic objectives and trade-offs from multiomics data. Results: Recent advances in single-cell omics, metabolic modeling, and machine/deep learning methods have enabled the inference of cellular objectives at both the transcriptomic and metabolic levels, bridging gene expression patterns with metabolic phenotypes. Conclusions: These in silico models provide insights into how cells adapt to changing environments, drug treatments, and genetic manipulations. We further explore the potential application of incorporating cellular objectives into personalized medicine, drug discovery, tissue engineering, and systems biology. Full article

Background/Objectives: Lauric acid (LA), a medium-chain fatty acid, is a promising drug for asthma treatment. This study evaluated the toxicity of repeated doses and the effect of LA on pulmonary ventilation and tracheal reactivity in asthmatic Wistar rats and identified possible molecular targets of LA action in silico. Methods: The rats were divided into control (CG) and LA-treated groups at 100 mg/kg (AL100G) for toxicity analysis. Pulmonary ventilation and tracheal reactivity were assessed in the control (CG), asthmatic (AG), asthmatic treated with LA at 25, 50, or 100 mg/kg (AAL25G, AAL50G, and AAL100G), and dexamethasone-treated groups (ADEXAG). Results: The results showed that LA at a dose of 100 mg/kg did not cause death or toxicity. A pulmonary ventilation analysis indicated that AG had reduced minute volume, which was prevented in AAL25G. LA at all doses prevented carbachol-induced tracheal hyper-responsiveness and reduced the relaxing effect of aminophylline, as observed in AG. An in silico analysis revealed that LA had a good affinity for nine proteins (β₂-adrenergic receptor, Ca_V, BK_Ca, K_ATP, adenylyl cyclase, PKG, eNOS, iNOS, and COX-2). Conclusions: LA at 100 mg/kg has low toxicity, prevents hyper-responsiveness in an asthma model in rats, and acts as a multitarget compound with a good affinity for proteins related to airway hyper-responsiveness. Full article

The discovery and development of new pharmaceutical drugs is a costly, time-consuming, and highly manual process, with significant challenges in ensuring drug bioavailability at target sites. Computational techniques are highly employed in drug design, particularly to predict the pharmacokinetic properties of molecules. One major kinetic challenge in central nervous system drug development is the permeation through the blood–brain barrier (BBB). Several different computational techniques are used to evaluate both BBB permeability and target delivery. Methods such as quantitative structure–activity relationships, machine learning models, molecular dynamics simulations, end-point free energy calculations, or transporter models have pros and cons for drug development, all contributing to a better understanding of a specific characteristic. Additionally, the design (assisted or not by computers) of prodrug and nanoparticle-based drug delivery systems can enhance BBB permeability by leveraging enzymatic activation and transporter-mediated uptake. Neuroactive peptide computational development is also a relevant field in drug design, since biopharmaceuticals are on the edge of drug discovery. By integrating these computational and formulation-based strategies, researchers can enhance the rational design of BBB-permeable drugs while minimizing off-target effects. This review is valuable for understanding BBB selectivity principles and the latest in silico and nanotechnological approaches for improving CNS drug delivery. Full article

Background: Resistance (R) genes are crucial for defending Perilla against pathogens like anthracnose, downy mildew, and phytophthora blight. Nucleotide-binding site leucine-rich repeat (NBS-LRR) genes, the largest R-gene family, play a central role in immunity. This study aimed to identify and characterize NBS-LRR genes in P. citriodora ‘Jeju17’. Methods: Previously conducted genome-wide data for ‘Jeju17’ were analyzed in silico to identify NBS-LRR genes. Results: A total of 535 NBS-LRR genes were identified, with clusters on chromosomes 2, 4, and 10. A unique RPW8-type R-gene was located on chromosome 7. Conclusions: This study provides insights into the NBS-LRR gene family in ‘Je-ju17’, highlighting its role in disease resistance and evolutionary dynamics. By identifying can-didate R-genes, this research supports breeding programs to develop disease-resistant cultivars and improves our understanding of plant immunity. Full article

Hyperuricemia arises from imbalanced uric acid metabolism, contributing to gout and related chronic diseases. When traditional drugs are used to treat hyperuricemia, side effects are inevitable, which promotes the exploration of new bioactive compounds. Protein hydrolysates and peptides are gradually showing potential in the treatment of hyperuricemia. This study investigated the uric acid inhibitory activity of peptides extracted from Trachurus japonicus using in silico and in vitro methods. We employed in silico virtual enzymolysis and experimental validation to identify bioactive peptides from Trachurus japonicus proteins. Four peptides (DF, AGF, QPSF, and AGDDAPR) were comprehensively screened by molecular docking and database analysis. After solid-phase synthesis, the inhibitory effects of these peptides on hyperuricemia were further verified in vitro and at the cellular level. The results showed that all four peptides have good hyperuricemia-inhibiting activities. Molecular docking and molecular dynamics revealed that peptides DF and AGDDAPR affect the production of uric acid by binding to the active sites of urate transporter 1 (URAT1), glucose transporter 9 (GLUT9), and xanthine oxidase (XOD), while peptides QPSF and AGF mainly influence the XOD active site, confirming that it is feasible to rapidly screen hyperuricemia-inhibiting peptides by molecular docking. Full article

Due to its central role in pain, inflammation, and related disorders, the Transient Receptor Potential (TPR) Vanilloid Type-1 (TRPV1) ion channel represents an attractive target for the development of novel antinociceptive and anti-inflammatory agents. Capsaicin, the natural component of chili peppers, is one of the most investigated agonists of this receptor. Several modifications of its structure have been attempted, aiming at finding TRPV1 agonists with improved characteristics, but, to date, no capsaicin-derived agents have reached the market. Based on our previous knowledge of the design and synthesis of TRPV1 agonists, in this paper we propose two small series of indole-2-carboxamides as novel and selective agonists for this ion channel. The newly developed compounds have been structurally characterized and tested in vitro for their ability to modulate TRPV1, in terms of efficacy, potency (EC₅₀), and desensitization (IC₅₀) properties. For the most promising derivatives, selectivity over the TRP ankyrin-1 (TRPA1) channel has been reported. From our study, compound 6g arose as a promising candidate for further evaluation, also in correlation with its in silico-predicted drug-like properties. Full article

Recently, SASH1 has emerged as a novel protein interactor of a few Eph tyrosine kinase receptors like EphA2. These interactions involve the first N-terminal Sam (sterile alpha motif) domain of SASH1 (SASH1-Sam1) and the Sam domain of Eph receptors. Currently, the functional meaning of the SASH1-Sam1/EphA2-Sam complex is unknown, but EphA2 is a well-established and crucial player in cancer onset and progression. Thus, herein, to investigate a possible correlation between the formation of the SASH1-Sam1/EphA2-Sam complex and EphA2 activity in cancer, cancer-linked mutations in SASH1-Sam1 were deeply analyzed. Our research plan relied first on searching the COSMIC database for cancer-related SASH1 variants carrying missense mutations in the Sam1 domain and then, through a variety of bioinformatic tools and molecular dynamic simulations, studying how these mutations could affect the stability of SASH1-Sam1 alone, leading eventually to a defective fold. Next, through docking studies, with the support of AlphaFold2 structure predictions, we investigated if/how mutations in SASH1-Sam1 could affect binding to EphA2-Sam. Our study, apart from presenting a solid multistep research protocol to analyze structural consequences related to cancer-associated protein variants with the support of cutting-edge artificial intelligence tools, suggests a few mutations that could more likely modulate the interaction between SASH1-Sam1 and EphA2-Sam. Full article

The development of new drugs is a lengthy and complex process regarding its conception and ideation, passing through in silico studies, synthesis, in vivo studies, clinical trials, approval, and commercialization, with an exceptionally low success rate. The lack of efficacy, safety, and suboptimal pharmacokinetic parameters are commonly identified as significant challenges in the discovery of new drugs. To help address these challenges, various approaches have been explored in medicinal chemistry, including the use of prodrug strategies. As a well-established approach, prodrug design remains the best option for improving physicochemical properties, reducing toxicity, and increasing selectivity, all while minimizing costs and saving on biological studies. This review article aims to analyze the current advances using the prodrug approach that has allowed the advance of drug candidates to clinical trials in the last 10 years. The approaches presented here aim to inspire further molecular optimization processes and highlight the potential of this strategy to facilitate the advancement of new compounds to clinical study phases. Full article

Bovine coronavirus (BCoV) exhibits dual tissue tropism, infecting both the respiratory and enteric tracts of cattle. Viral entry into host cells requires a coordinated interaction between viral and host proteins. However, the specific cellular receptors and co-receptors facilitating BCoV entry remain poorly understood. Similarly, the roles of host proteases such as Furin, TMPRSS2, and Cathepsin-L (CTS-L), known to assist in the replication of other coronaviruses, have not been extensively explored for BCoV. This study aims to identify novel BCoV receptors and host proteases that modulate viral replication and tissue tropism. Bovine cell lines were infected with BCoV isolates from enteric and respiratory origins, and the host cell gene expression profiles post-infection were analyzed using next-generation sequencing (NGS). Differentially expressed genes encoding potential receptors and proteases were further assessed using in-silico prediction and molecular docking analysis. These analyses focused on known coronavirus receptors, including ACE2, NRP1, DPP4, APN, AXL, and CEACAM1, to identify their potential roles in BCoV infection. Validation of these findings was performed using the qRT-PCR assays targeting individual genes. We confirmed the gene expression profiles of these receptors and enzymes in some BCoV (+/−) lung tissues. Results revealed high binding affinities of 9-O-acetylated sialic acid and NRP1 to BCoV spike (S) and hemagglutinin-esterase (HE) proteins compared to ACE2, DPP4, and CEACAM1. Additionally, Furin and TMPRSS2 were predicted to interact with the BCoV-S polybasic cleavage site (RRSRR|A), suggesting their roles in S glycoprotein activation. This is the first study to explore the interactions of BCoV with multiple host receptors and proteases. Functional studies are recommended to confirm their roles in BCoV infection and replication. Full article

Dysfunctional mitochondria are present in many neurodegenerative diseases, such as spinocerebellar ataxia type 3 (SCA3), also known as Machado–Joseph disease (MJD). SCA3/MJD, the most frequent neurodegenerative ataxia worldwide, is caused by the abnormal expansion of the polyglutamine tract (polyQ) at ataxin-3. This protein is known to deubiquitinate key proteins such as Parkin, which is required for mitophagy. Ataxin-3 also interacts with Beclin1 (essential for initiating autophagosome formation adjacent to mitochondria), as well as with the mitochondrial cristae protein TBK1. To identify other proteins of the mitophagy pathway (according to the KEGG database) that can interact with ataxin-3, here we developed a pipeline for in silico analyses of protein–protein interactions (PPIs), called auto-p2docking. Containerized in Docker, auto-p2docking ensures reproducibility and reduces the number of errors through its simplified configuration. Its architecture consists of 22 modules, here used to develop 12 protocols but that can be specified according to user needs. In this work, we identify 45 mitophagy proteins as putative ataxin-3 interactors (53% are novel), using ataxin-3 interacting regions for validation. Furthermore, we predict that ataxin-3 interactors from both Parkin-independent and -dependent mechanisms are affected by the polyQ expansion. Full article

The interest in new sources of bioactive compounds has been driven by the search for natural antioxidants capable of attenuating the toxicity of reactive oxygen species, as well as the emergence of pathogens resistant to antimicrobials. In this sense, we explored the potential of the macaúba epicarp. Compounds such as piceatannol, 3,4,5,3′,5′-penta-hydroxy-trans-stilbene (PHS), and in lower amounts, resveratrol were identified in extracts through techniques such as medium-pressure liquid chromatography, HPLC-MS, and imaging mass spectrometry (IMS), which confirmed the exclusive localization of PHS and piceatannol in the outer epicarp. Extraction with aqueous acetone (Me₂CO:H₂O) and its EtOAC fraction showed the highest yields of stilbenes and, moreover, it efficiently increased the tolerance of Saccharomyces cerevisiae to oxidative stress. Additionally, the Me₂CO:H₂O extract presented antibacterial and anti-cryptococcal activity, with piceatannol and resveratrol increasing survival rates of Galleria mellonella subjected to fungal infection. In silico ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis indicates low toxicity for piceatannol, PHS, and resveratrol, in addition to pharmacokinetic parameters that allow their use. These findings indicate the use of macaúba epicarp as a source of bioactive compounds valuable for the food, cosmetic, and pharmaceutical industries. Full article